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Series GSE59124 Query DataSets for GSE59124
Status Public on Mar 03, 2015
Title Sequential centromere shift via de novo formation in maize
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Overall design ChIP-seq was carried out with anti-CENH3 antibodies using material from young leaves with control, telo3-3 and its derivate.
 
Contributor(s) Han F, Birchler JA
Citation(s) 25733907
Submission date Jul 07, 2014
Last update date May 15, 2019
Contact name Handong Su
E-mail(s) shandong@mail.hzau.edu.cn
Phone +86-18810795796
Organization name Huazhong Agricultural University
Street address No.1,Shizishan Street ยท Hongshan District
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
 
Platforms (1)
GPL15463 Illumina HiSeq 2000 (Zea mays)
Samples (6)
GSM1428962 CENH3-ChIPseq-TB-9Sb
GSM1428963 CENH3-ChIPseq-telo2-2
GSM1428964 CENH3-ChIPseq-telo3-3
Relations
BioProject PRJNA254472
SRA SRP044103

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Supplementary file Size Download File type/resource
GSE59124_RAW.tar 1.6 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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