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| Status |
Public on Sep 17, 2019 |
| Title |
Transcriptome sequencing of HELZ-null HEK293T human cell line generated by CRISPR/Cas9 gene editing |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Eukaryotic SF1 helicases have been implicated in various aspects of RNA metabolism, including transcription, processing, translation, and degradation. Nevertheless, until now most human SF1 helicases remain poorly understood. Here, we have functionally and biochemically characterized the role of a putative SF1 helicase termed ‘Helicase with Zinc-finger’, or HELZ. We discovered that HELZ associates with various mRNA decay factors including components of the CCR4-NOT deadenylase complex in human and Drosophila melanogaster cells. The interaction between HELZ and the CCR4-NOT complex is direct and mediated by an extended low-complexity region in the C-terminal part of HELZ. We further reveal that HELZ uses the deadenylase complex to mediate translational repression and decapping-dependent mRNA decay. Transcriptome-wide analysis of HELZ-null cells suggests that HELZ has an important role in the regulation of the expression of genes associated with the development of the nervous system.
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| Overall design |
Two cell types with two biological replicates analysed using RNA-Seq
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| Contributor(s) |
Weber R, Igreja C |
| Citation(s) |
31570513 |
| Submission date |
Aug 07, 2019 |
| Last update date |
Oct 08, 2019 |
| Contact name |
Ramona Weber |
| E-mail(s) |
ramona.weber@uzh.ch
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| Organization name |
University of Zurich
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| Department |
Institute for Regenerative Medicine
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| Street address |
Wagistrasse 12
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| City |
Schlieren |
| ZIP/Postal code |
8952 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
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| Samples (4)
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| GSM4013201 |
HEK293T, Wild-type replicate 1 for RNA-seq |
| GSM4013202 |
HEK293T, Wild-type replicate 2 for RNA-seq |
| GSM4013203 |
HEK293T, HELZ-null replicate 1 for RNA-seq |
| GSM4013204 |
HEK293T, HELZ-null replicate 2 for RNA-seq |
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| Relations |
| BioProject |
PRJNA559139 |
| SRA |
SRP217693 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135505_DE_HELZ_vs_WT.txt.gz |
404.9 Kb |
(ftp)(http) |
TXT |
| GSE135505_readcounts_unfiltered.txt.gz |
286.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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