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Series GSE155245 Query DataSets for GSE155245
Status Public on Jan 22, 2021
Title Divergence in alternative polyadenylation between humans and chimpanzees contributes to gene regulatory differences between species
Organisms Pan troglodytes; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary Differences in gene regulation contribute to phenotypic differences between humans and other primates. While co-transcriptional gene regulatory mechanisms such as alternative polyadenylation (APA) can help explain how variation in gene regulation manifests, such mechanisms remain understudied. We measured polyadenylation site (PAS) usage in a panel of 6 human and 6 chimpanzee lymphoblastoid cell lines (LCLs). While APA is largely conserved between humans and chimpanzees, genes with divergent APA patterns are enriched among differentially expressed and differentially translated genes. Differential usage of 3’ UTR and intronic PAS are both significantly correlated with differential mRNA expression effect sizes but in opposite directions. For many genes, there is one PAS dominant, meaning it is used much more often than others. The dominant PAS for these gene is overwhelmingly shared between species, however, differences in dominant PAS are enriched for genes with expression differences. Finally, through post-translational mechanisms, we believe APA contributes to genes differentially expressed at the protein level but not in mRNA. As this is the first primate comparative study of APA, our study establishes APA as a key mechanism underlying the genetic regulation of gene and protein expression levels in primates.
 
Overall design We measured polyadenylation site (PAS) usage in a panel of 6 human and 6 chimpanzee lymphoblastoid cell lines (LCLs). We collected 3' Seq on total and nuclear mRNA using the Lexogen Rev Quant Seq protocol. We collected RNA sequencing on the total mRNA using the Illumina TruSeq kit.
 
Contributor(s) Mittleman B, Pott S, Warland S, Barr K, Cuevas C, Gilad Y
Citation(s) 33595436
Submission date Jul 28, 2020
Last update date Mar 23, 2021
Contact name Yoav GiladLi
E-mail(s) gilad@uchicago.edu
Organization name University of Chicago
Department Section of Genetic Medicine
Lab Gilad
Street address 920 e 58th St
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL21121 Illumina NextSeq 500 (Pan troglodytes)
Samples (23)
GSM4698121 18498_Nuclear RNA
GSM4698122 18498_Total RNA
GSM4698123 18499_Total RNA
Relations
BioProject PRJNA649122
SRA SRP273904

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Supplementary file Size Download File type/resource
GSE155245_PAS_GeneLocation.txt.gz 209.5 Kb (ftp)(http) TXT
GSE155245_PAS_doublefilter_either_ChimpCoordChimpUsage.sort.bed.gz 597.9 Kb (ftp)(http) BED
GSE155245_PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed.gz 561.3 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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