|
| Status |
Public on Mar 01, 2018 |
| Title |
Functional analysis of HD2C in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
Ribosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis histone deacetylase HD2C in pre-rRNA processing via both canonical and non-canonical manners. HD2C interacts with HD2B and forms homo- and/or hetero-oligomers in the nucleolus. Depletion of HD2C and HD2B induces a ribosome biogenesis deficiency morphological phenotype and aberrant accumulation of 18S pre-rRNA intermediates. Our genome-wide analysis revealed that HD2C binds and represses the expression of key genes involved in ribosome biogenesis. Using RNA immunoprecipitation and sequencing, we further uncovered a non-canonical mechanism of HD2C directly associating with pre-rRNA and small nucleolar RNAs to regulate rRNA methylation. Together, this study reveals a multifaceted role of HD2C in ribosome biogenesis and provides mechanistic insights into how histone deacetylases modulate rRNA maturation at both transcriptional and post-transcriptional levels.
|
| |
|
| Overall design |
HD2C binding site were studied with ChIP-seq; Gene expression change in hd2b hd2c double mutant was studied using RNA-seq; H4K16 hyperacetylation site were identtified with H4K16ac ChIP-seq in hd2c mutant; HD2C binding RNAs were identified with HD2C RIP-seq.
|
| |
|
| Contributor(s) |
Lu L, Chen X, Zhong X |
| Citation(s) |
29343504 |
| Submission date |
Dec 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuehua Zhong |
| Organization name |
Wisconsin Institute for Discovery
|
| Department |
Epigenetics
|
| Street address |
330 N. Orchard St.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
|
| Samples (9)
|
|
| Relations |
| BioProject |
PRJNA421832 |
| SRA |
SRP126460 |
Less...
More...