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| Status |
Public on Mar 23, 2016 |
| Title |
KDM5 Lysine Demethylases Are Involved in Maintenance of 3'UTR Length [RNA-Seq] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We discovered that the Saccharomyces cerevisiae lysine demethylase, Jhd2 (also known as KDM5), recruits 3'UTR processing machinery and promotes alteration of 3'UTR length in a demethylase-dependent manner. Interaction of Jhd2 with both chromatin and RNA suggests that Jhd2 affects selection of polyadenylation sites through a transcription-coupled mechanism.
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| Overall design |
For 3'READs analysis, wild-type yeast or yeast with JHD2 deleted were grown to mid-log phase and RNA was extracted as mentioned above. cDNA libraries enriched for 3'UTRs were prepared as previously published and as noted in Figure 4a [28]. Samples were then subjected to RNA sequencing on the Illumina Hiseq 2000 using 50bp single end reads. Data was analyzed as previously [Hoque M] with the following modifications: The adapter sequences were trimmed off the single-ended reads. The remaining reads longer than 15 bp were mapped to yeast genome SacCer3 using bowtie2 [Langmead B 2012] with the setting '-5 4 --local', trimming off 4bp from 5' and allowing soft clipping (S) at both ends. The alignments were then filtered by 1) MAPQ>=10, 2) mismatches <= 5%, 3) unaligned 5' Ts >=2 to get the PASS reads. The last aligned positions of the PASS reads were grouped to pA clusters with a clustering size of 24 bp. Each pA cluster was assigned to one of the genes defined by SGD [Cherry JM]. The 3' end of a gene was extended 1000bp from the end of CDS until it overlaps with another gene in the same direction. The pA Clusters were then filtered by contains 1) >= 3 PASS reads 2) >= 5% of all PASS reads mapped to the gene.
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| Contributor(s) |
Blair LP, Liu Z, Zheng D, Tian B, Yan Q |
| Citation(s) |
28138513 |
| Submission date |
Mar 23, 2015 |
| Last update date |
Jun 26, 2019 |
| Contact name |
Zongzhi Liu |
| E-mail(s) |
zongzhi.liu@yale.edu
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| Phone |
2039032599
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| Organization name |
yale university
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| Street address |
310 Cedar Street
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| City |
new haven |
| State/province |
CONNECTICUT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE67212 |
KDM5 Lysine Demethylases Are Involved in Maintenance of 3'UTR Length |
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| Relations |
| BioProject |
PRJNA279141 |
| SRA |
SRP056425 |
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