Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic characteristics and gene-expression analysis of a de novo centromere in maize

ABSTRACT: De novo centromeres originate occasionally from non-centromeric regions of chromosomes, providing an excellent model system to study centromeric chromatin. The maize mini-chromosome Dp3a contains a de novo centromere, which was derived from a euchromatic site on the long arm of chromosome 3 that lacks traditional centromeric repeat sequences. Our previous study found that the CENH3 binding domain of this de novo centromere is only 350 kb with a high-density gene distribution with low-density of transposons. Here we analyzed the kinetochore complex assembled on the de novo centromere, which revealed that it resembles the native centromeres. Meiotic analyses showed that the Dp3a mini-chromosome formed bi-orientation during meiosis I and could stably transmit through meiosis. We applied next generation sequencing technology to analyze gene transcription, DNA methylation and histone modifications for this region. Our RNA-seq data revealed that active chromatin is not a barrier for de novo centromere formation. The gene expression level within the Dp3a breakpoints of native chromosome 3 indicated a gene dosage effect due to the additional copy of Dp3a mini-chromosome region in chromosome 3. Bisulfite-ChIP-seq results indicate a slightly increased DNA methylation level after de novo centromere formation, reaching the level of a native centromere. No strand-specific bias of DNA methylation was found at maize native and Dp3a de novo centromeres. H2A-T133 phosphorylation occurs in the CENH3 nucleosome. These results provide insight into the mechanism of de novo centromere formation and subsequent consequences.

ORGANISM(S): Zea mays

PROVIDER: GSE64641 | GEO | 2016/12/01

SECONDARY ACCESSION(S): PRJNA271532

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Epigenetic characteristics and gene-expression analysis of Derivative 3-3 de novo centromere in maize

Project description:De novo centromeres originate occasionally from non-centromeric regions of chromosomes, providing an excellent model system to study centromeric chromatin. The maize mini-chromosome Derivative 3-3 contains a de novo centromere, which was derived from a euchromatic site on the short arm of chromosome 9 that lacks traditional centromeric repeat sequences. Our previous study found that the CENH3 binding domain of this de novo centromere is only 288 kb with a high-density gene distribution with low-density of transposons. Here we applied next generation sequencing technology to analyze gene transcription, DNA methylation for this region. Our RNA-seq data revealed that active chromatin is not a barrier for de novo centromere formation. Bisulfite-ChIP-seq results indicate a slightly increased DNA methylation level after de novo centromere formation, reaching the level of a native centromere. These results provide insight into the mechanism of de novo centromere formation and subsequent consequences. RNA-seq was carried out using material from seedling and young leaves between control and Derivative 3-3. Bisulfite-ChIP-seq was carried out with anti-CENH3 antibodies using material from young leaves in Derivative 3-3.

2016-08-05 | E-GEOD-76533 | biostudies-arrayexpress

Epigenetic characteristics and gene-expression analysis of Derivative 3-3 de novo centromere in maize

2016-08-05 | GSE76533 | GEO

Sequential centromere shift via de novo formation in maize

Project description:The ability of centromeres to alternate between active and inactive states indicates significant epigenetic elements controlling centromere assembly and centromere function. In maize (Zea mays), misdivision of the B chromosome centromere on a translocation with the short arm of chromosome 9 (TB-9Sb) can produce many variants with varying centromere sizes and centromeric DNA sequences. In derivatives of TB-9Sb, we found a de novo centromere on chromosome telo-3-3, which has no canonical centromeric repeat sequences. This centromere is derived from a 288-kb region on the short arm of chromosome 9, and is 19 megabases (Mb) removed from the translocation breakpoint of chromosome 9 in TB-9Sb. This centromere is much smaller than normal ones but can be maintained through meiosis. The functional B centromere in progenitor telo2-2 is deleted from telo3-3 but some B-repeat sequences remain. The de novo centromere of telo3-3 becomes inactive in three further derivatives with new centromeres being formed elsewhere on the chromosomes. One such de novo centromere contains only 200-kb CENH3 binding domain. This 200-kb centromere is located 3 Mb removed from the translocation breakpoint in a new location. The deleted B centromere in telo3-3 is activated in two derivatives. Our results suggest that de novo centromere formation is more common than previously thought and can persist on chromosomal fragments without a canonical centromere providing implications for karyotype evolution. ChIP-seq was carried out with anti-CENH3 antibodies using material from young leaves with control, telo3-3 and its derivate.

2015-03-03 | E-GEOD-59124 | biostudies-arrayexpress

Sequential centromere shift via de novo formation in maize

2015-03-03 | GSE59124 | GEO

ChIP-seq in oat-maize additional lines using CenH3 antibody

Project description:Many existing centromeres may have originated as neocentromeres that activated de novo from non-centromeric regions. However, the evolutionary path from a neocentromere to a mature centromere has been elusive. Here we analyzed the centromeres of six chromosomes that were transferred from maize into oat as the result of an inter-species cross. Centromere size and location were assayed by chromatin immunoprecipitation for the histone variant CENH3, which is a defining feature of functional centromeres. Maize and oat are highly divergent and differ in genome size by four fold. Two isolates of maize chromosome proved to contain neocentromeres in the sense that they had moved from the original site, whereas the remaining seven centromeres (1, 2, 5, 6, 8, 9 and 10) were retained in the same area in both species. In all cases the CENH3-binding domains were dramatically expanded to encompass a larger area in the oat background (~4 Mb) than the average centromere size in maize (~2 Mb). The expansion of maize centromeres appeared to be restricted by the transcription of genes located in regions flanking the original centromeres. The results from the current study provide evidence that (1) centromere size is regulated; (2) centromere sizes tend to be uniform within a species regardless of chromosome size or origin of the centromere; and (3) neocentromeres emerge and expand preferentially in gene poor regions. Our results, together with data from several animal species, suggest that centromere size expansion may be a key factor in the survival of neocentric chromosomes in natural populations.

2013-09-01 | GSE47342 | GEO

De novo formation in maize from irradiated materials

Project description:In maize (Zea mays), irradiation can produce many variants with varying centromeric DNA sequences. We found de novo centromeres in F3-152 and F3-600, which has no canonical centromeric repeat sequences. This centromere is derived from a 1520-kb and 188-kb region on the arm of chromosome 10 and 3. Our results suggest that de novo centromere formation is more common than previously thought and can persist on chromosomal fragments without a canonical centromere providing implications for karyotype evolution.

2019-12-21 | GSE124242 | GEO

Centromere misdivision promotes centromeric sequence changes, de novo centromere formation, and centromere expansion

Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids. ChIP-seq was carried out with anti-CENH3 antibody using material 4DS and control (Chinese Spring, CS as short).

2016-04-02 | E-GEOD-63752 | biostudies-arrayexpress

Functional centromere lost centromeric specific sequences but gain new sequences from nearby chromosomal arm.

Project description:We identified a newly formed dicentric chromosome (sDic-15) in maize from intrachromosomal recombination and BFB cycles, in which only one centromere is active. The centromeres lost CentC sequences and dramatic reduced the CRM sequences, but when the molecular features of functional centromeres such as CENH3 was examined, they were present. Immunolocalization analysis of phosphorylation of H3T3, H3ser-10 and H2A levels on this new centromere shows a pattern typical of a functional centromere. Meiotic analysis revealed that this dicentric chromosome is table and transmit very well. To examine the new sequences associated with CENH3 in this centromere, chromatin immunoprecipitation (ChIP) was carried out with anti-CENH3 antibodies and material from young seedlings with or without dicentric chromosome. We mapped the ChIP-Seq reads to the reference genome and found a 723kb region from the short arm of maize chromosome 9 involve the new centromere formation. This region is gene-poor and full of TEs, but genes in this region are transcribed. The original 723kb region shows a high DNA methylation level as native centromeres but had no significant change when it involved into new centromere formation. The reactivation of this newly formed centromere indicated that centromere reactivation may not dependent on the relatively intact DNA sequences or topology of original inactive centromere.

2013-06-25 | GSE43140 | GEO

Functional centromere lost centromeric specific sequences but gain new sequences from nearby chromosomal arm.

2013-06-25 | E-GEOD-43140 | biostudies-arrayexpress

Structure, composition and evolution of the nonvital B chromosome of maize

Project description:To determine the centromere of the maize B chromosome, we used previously published anti-CENH3-ChIP-seq data from TB-9Sb, which contain a complete functional B centromere. Distribution of centromere-specific DNA repeats, including CentC, CRM element and B-repeat, were observed in the proximal end of the assembled maize B chromosome, and this region was shown to be associated with CENH3 nucleosomes. Furthermore, six small scaffolds with sizes ranging from 10 to 174 kilobase display CENH3 enrichment, also with the distribution of these repeat sequences. These results were consistent with previously cytogenetic observation. Therefore, approximately 520 kb centromeric regions were determined in the assembled maize B chromosome.

2021-05-22 | GSE152074 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data