GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE85009 Query DataSets for GSE85009
Status Public on Feb 16, 2017
Title ZSCAN5B and its primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression [Human cell line ChIP-Seq data set]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Particularly in the context of differentiation and development, the importance of three-dimensional chromatin architecture to gene regulatory mechanisms is becoming increasingly clear. The most ancient known mechanism of chromatin organization involves TFIIIC, a transcription factor (TF) that recruits RNA polymerase III (Pol III) for transcription of tRNA and other types of non-coding RNA genes. From yeast to mammals, TFIIIC binds to tRNA genes (tDNAs) and scattered “extra-TFIIIC” (ETC) loci and serves to tether these loci together as anchors of chromatin loops. TFIIIC activities are modulated by MAF, MYC, and other TF proteins that are still unidentified. Here we identify the ZSCAN5 TF family - including mammalian ZSCAN5B and its primate-specific paralogs - as proteins that occupy mammalian Pol III promoters and ETC sites. We show that ZSCAN5B binds with high specificity to a conserved subset of tDNA loci and other Pol III genes in human and mouse and that primate-specific ZSCAN5A and ZSCAN5D also bind Pol III genes, although ZSCAN5D preferentially localizes to MIR SINE- and LINE2-associated ETC sites. ZSCAN5 genes are expressed in proliferating cell populations and are cell-cycle regulated, and gene expression data suggested that they might cooperate to regulate basic cellular functions including mitotic progression. Consistent with this predicted role, ZSCAN5A knockdown led to increasing numbers of cells in mitotic cells and aneuploidy in cultured cells. Together these data implicate ZSCAN5 genes in regulation of Pol III gene transcription and nearby Pol II genes, ultimately influencing cell cycle progression and differentiation in a variety of tissues.
Overall design Antibodies specific to ZCSAN5A, ZCSAN5B and ZCSAN5D were used in Chromatin immunoprecipitation (ChIP) experiments in chromatin from the BeWo choriocarcinoma cells; ZSCAN5B was also used in HEK 293 human embryonic kidney cell lines. Experiments were done in duplicate and compared to genomic input controls.
Contributor(s) Stubbs L, Sun Y
Citation(s) 27732952
Submission date Jul 29, 2016
Last update date May 15, 2019
Contact name Lisa J Stubbs
Organization name University of Illinois Urbana-Champaign
Department IGB
Lab Stubbs Lab
Street address 1206 West Gregory Drive | MC-195
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (11)
GSM2255819 19_HEK_ZSCAN5B_SC
GSM2255820 20_HEK_ZSCAN5B_SC
GSM2255821 22_HEK_input
This SubSeries is part of SuperSeries:
GSE85045 ZSCAN5B and its primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression
BioProject PRJNA336019
SRA SRP080752

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE85009_10_11_BeWo_ZSCAN5B_SC_pooled_16_BeWo_input_control_MACS142_treat_all.wig.gz 302.7 Mb (ftp)(http) WIG
GSE85009_19_20_HEK_ZSCAN5B_SC_pooled_22_HEK_input_control_MACS142_treat_all.wig.gz 404.2 Mb (ftp)(http) WIG
GSE85009_RAW.tar 1.6 Gb (http)(custom) TAR (of WIG)
GSE85009_pooled_11-BeWo-ZSCAN5D_28-BeWo-ZSCAN5D_MACS142_treat_all.wig.gz 302.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap