scholarly journals CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA

2002 ◽  
Vol 159 (5) ◽  
pp. 765-775 ◽  
Author(s):  
Jun-ichirou Ohzeki ◽  
Megumi Nakano ◽  
Teruaki Okada ◽  
Hiroshi Masumoto
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
De Novo ◽  
Repetitive Sequences ◽  
Point Mutations ◽  
Artificial Chromosome ◽  
Binding Activity ◽  
Chromatin Assembly ◽  
Direct Assembly ◽  
Alphoid Dna

Centromere protein (CENP) B boxes, recognition sequences of CENP-B, appear at regular intervals in human centromeric α-satellite DNA (alphoid DNA). In this study, to determine whether information carried by the primary sequence of alphoid DNA is involved in assembly of functional human centromeres, we created four kinds of synthetic repetitive sequences: modified alphoid DNA with point mutations in all CENP-B boxes, resulting in loss of all CENP-B binding activity; unmodified alphoid DNA containing functional CENP-B boxes; and nonalphoid repetitive DNA sequences with or without functional CENP-B boxes. These four synthetic repetitive DNAs were introduced into cultured human cells (HT1080), and de novo centromere assembly was assessed using the mammalian artificial chromosome (MAC) formation assay. We found that both the CENP-B box and the alphoid DNA sequence are required for de novo MAC formation and assembly of functional centromere components such as CENP-A, CENP-C, and CENP-E. Using the chromatin immunoprecipitation assay, we found that direct assembly of CENP-A and CENP-B in cells with synthetic alphoid DNA required functional CENP-B boxes. To the best of our knowledge, this is the first reported evidence of a functional molecular link between a centromere-specific DNA sequence and centromeric chromatin assembly in humans.

scholarly journals DNA Sequence Preference for De Novo Centromere Formation on a Caenorhabditis elegans Artificial Chromosome

2020 ◽  
Author(s):  
Zhongyang Lin ◽  
Karen Wing Yee Yuen
Keyword(s):  
Caenorhabditis Elegans ◽  
Dna Sequence ◽  
Dna Sequences ◽  
De Novo ◽  
Repetitive Sequences ◽  
Model Organism ◽  
Artificial Chromosome ◽  
Centromeric Dna ◽  
Artificial Chromosomes ◽  
Non Homologous End Joining

ABSTRACTCentromeric DNA sequences vary in different species, but share common characteristics, like high AT-content, repetitiveness, and low, but not no, transcriptional activity. Yet, neocentromeres can be found on non-centromeric, ectopic sequences, suggesting that centromeres can be established and maintained epigenetically. In contrast, canonical centromeric DNA sequences are more competent in de novo centromere formation on artificial chromosomes (ACs). To determine if specific DNA sequence features are preferred for new centromere formation, we injected different DNA sequences into the gonad of a holocentric model organism, Caenorhabditis elegans, to form ACs in embryos, and monitored mitotic AC segregation. We demonstrated that AT-rich sequences, but not repetitive sequences, accelerated de novo centromere formation on ACs. We also injected fragmented Saccharomyces cerevisiae genomic DNA to construct a less repetitive, more complex AC that can propagate through generations. By whole-genome sequencing and de novo assembly of AC sequences, we deduced that this AC was formed through non-homologous end joining. By CENP-AHCP-3 chromatin immunoprecipitation followed by sequencing (ChIP-seq), we found that CENP-AHCP-3 domain width on both the AC and endogenous chromosomes is positively correlated with AT-content. Besides, CENP-AHCP-3 binds to unexpressed gene loci or non-genic regions on the AC, consistent with the organization of endogenous holocentromeres.

A mushroom-inducing DNA sequence isolated from the Basidiomycete, Schizophyllum commune.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 707-716 ◽  
Author(s):  
J S Horton ◽  
C A Raper
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
De Novo ◽  
Schizophyllum Commune ◽  
Sequence Divergence ◽  
Fruiting Bodies ◽  
Genomic Dnas ◽  
Different Strains ◽  
Mating Interaction ◽  
Normal Requirement

Abstract A DNA sequence capable of inducing the de novo development of fruiting bodies (mushrooms) when integrated into the genome of unmated, nonfruiting strains of the Basidiomycete Schizophyllum commune has been isolated and partially characterized. This sequence, designated FRT1, overrides the normal requirement of a mating interaction for fruiting in this organism. It has been shown to integrate stably in different chromosome locations and appears to be trans-acting. It also enhances the normal process of fruiting that occurs after mating. Additional DNA sequences with similarity to FRT1 were detected within the genome of the strain of origin by hybridization of labeled FRT1 DNA to blots of digested genomic DNAs. FRT1 and the genomic sequences similar to it were shown to be genetically linked. Southern hybridization experiments suggested sequence divergence at the FRT1 locus between different strains of S. commune. A testable model for how FRT1 may act as a key element in the pathway for the differentiation of fruiting bodies is presented as a working hypothesis for further investigation.

scholarly journals HERP, a Novel Heterodimer Partner of HES/E(spl) in Notch Signaling

2001 ◽  
Vol 21 (17) ◽  
pp. 6080-6089 ◽  
Author(s):  
Tatsuya Iso ◽  
Vittorio Sartorelli ◽  
Coralie Poizat ◽  
Simona Iezzi ◽  
Hung-Yi Wu ◽  
...  
Keyword(s):  
Dna Binding ◽  
Notch Signaling ◽  
Dna Sequences ◽  
Transcriptional Repression ◽  
De Novo ◽  
Single Cells ◽  
Binding Activity ◽  
Bhlh Protein ◽  
Helix Loop Helix ◽  
Dna Binding Activity

ABSTRACT HERP1 and -2 are members of a new basic helix-loop-helix (bHLH) protein family closely related to HES/E(spl), the only previously known Notch effector. Like that of HES, HERP mRNA expression is directly up-regulated by Notch ligand binding without de novo protein synthesis. HES and HERP are individually expressed in certain cells, but they are also coexpressed within single cells after Notch stimulation. Here, we show that HERP has intrinsic transcriptional repression activity. Transcriptional repression by HES/E(spl) entails the recruitment of the corepressor TLE/Groucho via a conserved WRPW motif, whereas unexpectedly the corresponding—but modified—tetrapeptide motif in HERP confers marginal repression. Rather, HERP uses its bHLH domain to recruit the mSin3 complex containing histone deacetylase HDAC1 and an additional corepressor, N-CoR, to mediate repression. HES and HERP homodimers bind similar DNA sequences, but with distinct sequence preferences, and they repress transcription from specific DNA binding sites. Importantly, HES and HERP associate with each other in solution and form a stable HES-HERP heterodimer upon DNA binding. HES-HERP heterodimers have both a greater DNA binding activity and a stronger repression activity than do the respective homodimers. Thus, Notch signaling relies on cooperation between HES and HERP, two transcriptional repressors with distinctive repression mechanisms which, either as homo- or as heterodimers, regulate target gene expression.

Structure and evolution of the Cinful retrotransposon family of maize

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 745-752 ◽  
Author(s):  
Soledad Sanz-Alferez ◽  
Phillip SanMiguel ◽  
Young-Kwan Jin ◽  
Patricia S Springer ◽  
Jeffrey L Bennetzen
Keyword(s):  
Tandem Repeats ◽  
Yeast Artificial Chromosome ◽  
Repetitive Sequences ◽  
Point Mutations ◽  
Sequence Divergence ◽  
Artificial Chromosome ◽  
Major Constituent ◽  
Apparent Lack ◽  
Gene Acquisition ◽  
Functional Components

A maize cDNA clone was isolated by virtue of its intense hybridization to total maize genomic DNA, indicating homology to highly repetitive sequences. Genomic homologues were identified and subcloned from an adh1-bearing maize yeast artificial chromosome (YAC). Sequencing revealed that the expressed sequence was part of a Ty3-gypsy-type retrotransposon. We discovered and sequenced two complete retrotransposons of this family, and named them Cinful elements because they are members of a family of maize retrotransposons including Zeon-1 and the first plant transposable element sequenced, the solo long terminal repeat (LTR) called Cin1. All are defective, as Cinful-1 and Cinful-2 elements lack gag and Zeon-1 lacks pol homology. Despite the apparent lack of an intact "autonomous" element, the Cinful family has expanded to a copy number of about 18 000, representing just under 9% of the maize genome. Both point mutations and major rearrangements, including possible gene acquisition, differentiate members of the Cinful family. Cinful family members were found to have an unusual feature that we also observed in two other Ty3-class retrotransposons of teosinte and tobacco: related tandem repeats that separate their internal domains with a gag- or pol-containing homology from a 3' segment of unknown function. The conserved and variable features identified provide insights into the origin, mutational history, and functional components of this major constituent of the maize genome.Key words: Cin1, genome evolution, sequence divergence, Ty3-gypsy elements, Zeon-1.

scholarly journals 391. De Novo Human Artificial Chromosome Formation Is Predetermined by Initial Chromatin Assembly and Transcriptional Patterns after Transfection

2006 ◽  
Vol 13 ◽  
pp. S149
Author(s):  
Hiroshi Nakashima ◽  
Megumi Nakano ◽  
Ryoko Ohnishi ◽  
Yasushi Hiraoka ◽  
Yasufumi Kaneda ◽  
...  
Keyword(s):  
De Novo ◽  
Artificial Chromosome ◽  
Chromatin Assembly ◽  
Human Artificial Chromosome ◽  
Chromosome Formation

scholarly journals CENP-B creates alternative epigenetic chromatin states permissive for CENP-A or heterochromatin assembly

2020 ◽  
Vol 133 (15) ◽  
pp. jcs243303 ◽  
Author(s):  
Koichiro Otake ◽  
Jun-ichirou Ohzeki ◽  
Nobuaki Shono ◽  
Kazuto Kugou ◽  
Koei Okazaki ◽  
...  
Keyword(s):  
De Novo ◽  
Artificial Chromosome ◽  
Human Artificial Chromosome ◽  
Open Chromatin ◽  
Histone Chaperones ◽  
Satellite Dnas ◽  
Chromatin States ◽  
Heterochromatin Formation ◽  
Acidic Domain ◽  
Alphoid Dna

ABSTRACTCENP-B binds to CENP-B boxes on centromeric satellite DNAs (known as alphoid DNA in humans). CENP-B maintains kinetochore function through interactions with CENP-A nucleosomes and CENP-C. CENP-B binding to transfected alphoid DNA can induce de novo CENP-A assembly, functional centromere and kinetochore formation, and subsequent human artificial chromosome (HAC) formation. Furthermore, CENP-B also facilitates H3K9 (histone H3 lysine 9) trimethylation on alphoid DNA, mediated by Suv39h1, at ectopic alphoid DNA integration sites. Excessive heterochromatin invasion into centromere chromatin suppresses CENP-A assembly. It is unclear how CENP-B controls such different chromatin states. Here, we show that the CENP-B acidic domain recruits histone chaperones and many chromatin modifiers, including the H3K36 methylase ASH1L, as well as the heterochromatin components Suv39h1 and HP1 (HP1α, β and γ, also known as CBX5, CBX1 and CBX3, respectively). ASH1L facilitates the formation of open chromatin competent for CENP-A assembly on alphoid DNA. These results indicate that CENP-B is a nexus for histone modifiers that alternatively promote or suppress CENP-A assembly by mutually exclusive mechanisms. Besides the DNA-binding domain, the CENP-B acidic domain also facilitates CENP-A assembly de novo on transfected alphoid DNA. CENP-B therefore balances CENP-A assembly and heterochromatin formation on satellite DNA.

CUMULATIVE SPECTRAL REPEAT FINDER (CSRF): A SPECTRAL APPROACH FOR IDENTIFYING THE LENGTH OF REPEATS IN DNA SEQUENCES

2011 ◽  
Vol 20 (01) ◽  
pp. 179-194
Author(s):  
R. M. CHEN ◽  
M. T. HOU ◽  
N. W. CHANG ◽  
Y. T. CHEN ◽  
JEFFREY J. P. TSAI
Keyword(s):  
Dna Sequence ◽  
Gibbs Sampler ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Exact Method ◽  
Spectral Approach ◽  
Copy Numbers ◽  
Rules Of Thumb

Repetitive sequences of DNA are meaningful and of great importance to human functions. Previous researchers have proposed various methods to discover repetitive sequences in DNA sequence. However, the unknown lengths for repetitive sequences are usually predicted randomly or determined by rules of thumb rather than using a systematical criterion. We propose a new algorithm based on the cumulative Fourier spectral contents of DNA sequence to identify the candidate lengths of repetitive sequences or repeats in DNA sequences. After the candidate lengths of repeats are known, one can identify the repeats and their copy numbers using an exact method. Both of the simulated and real datasets are used to illustrate the performance of the proposed algorithm. The results are also compared to two well-known methods such as Spectral Repeat Finder (SRF) and Gibbs sampler. Furthermore, we demonstrate the use of CSRF in some well-known repeats-finding methods such as SRF, Gibbs sampler, MEME.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Sign in / Sign up

Export Citation Format

Share Document