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| Status |
Public on Aug 24, 2024 |
| Title |
RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [RNA-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The centromere is a pivotal chromatin domain that ensures accurate chromosome segregation during cell division. However, the epigenome regulation of the centromere and its impact on centromere function remain largely elusive. Here in the model plant Arabidopsis, we show that CCR4, the catalytic subunit of the RNA deadenylation complex CCR4-NOT, is essential for maintenance of the centromere epigenome and chromosome integrity. We demonstrate that CCR4 is involved in shortening of the poly(A) tails of transcripts originated from centromeric transposons and repeats, thereby promoting the production of small interfering RNAs (siRNAs). The CCR4-dependent siRNAs guide non-CG DNA methylation at centromere repeats, and CCR4 cooperates with canonical DNA methylation pathways to enhance centromeric H3K9 methylation and ensure mitotic chromosome stability. Our study illustrates the crucial role of RNA quality control in RNA interference and reveals the elaborate mechanism that safeguards plant centromeres through epigenomic regulation.
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| Overall design |
Three biological replicates of RNA-seq samples using 12-day-old seedlings in WT, ccr4a ccr4b, ddm1rdr2, ddm1 rdr2 ccr4a ccr4b, ddm1 rdr2 rdr6.
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| Contributor(s) |
Shimada A, Saze H |
| Citation missing |
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| Submission date |
Aug 07, 2024 |
| Last update date |
Aug 26, 2024 |
| Contact name |
ATSUSHI SHIMADA |
| Organization name |
Okinawa Institute of Science and Technology
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| Department |
Plant Epigenetics Unit
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| Lab |
Saze Lab
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| Street address |
1919-1 Tancha
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| City |
Onna-son, Kunigami-gun, Okinawa |
| ZIP/Postal code |
904-0495 |
| Country |
Japan |
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| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (15)
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| GSM8444853 |
RNA-seq, ccr4a ccr4b, seedlings, rep1 |
| GSM8444854 |
RNA-seq, ccr4a ccr4b, seedlings, rep2 |
| GSM8444855 |
RNA-seq, ccr4a ccr4b, seedlings, rep3 |
| GSM8444856 |
RNA-seq, ddm1 rdr2, seedlings, rep1 |
| GSM8444857 |
RNA-seq, ddm1 rdr2, seedlings, rep2 |
| GSM8444858 |
RNA-seq, ddm1 rdr2, seedlings, rep3 |
| GSM8444859 |
RNA-seq, ccr4a ccr4b ddm1 rdr2, seedlings, rep1 |
| GSM8444860 |
RNA-seq, ccr4a ccr4b ddm1 rdr2, seedlings, rep2 |
| GSM8444861 |
RNA-seq, ccr4a ccr4b ddm1 rdr2, seedlings, rep3 |
| GSM8444862 |
RNA-seq, ddm1 rdr2 rdr6, seedlings, rep1 |
| GSM8444863 |
RNA-seq, ddm1 rdr2 rdr6, seedlings, rep2 |
| GSM8444864 |
RNA-seq, ddm1 rdr2 rdr6, seedlings, rep3 |
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| Relations |
| BioProject |
PRJNA1145380 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE274191_RAW.tar |
71.1 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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