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Series GSE224753 Query DataSets for GSE224753
Status Public on Jul 02, 2023
Title Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation [ChiP-seq 3]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The P-TEFb-containing super elongation complex (SEC) plays the essential role in transcriptional elongation control. The AF4/FMR2 family members AFF1 and AFF4 are the central scaffold proteins of SEC, associated with different human diseases. However, their specific roles in transcriptional control remain unclear. Here, we report that AFF1 and AFF4 show distinct genomic distribution patterns around TSS. AFF1 binds upstream of TSS, while AFF4 is enriched downstream of TSS. Pol II occupancies are reduced genome-widely after depletion of AFF1, but not AFF4. Interestingly, in a subset of active genes with broad AFF4 binding signature, AFF4 disruption causes slow elongation and early termination, while AFF1 deletion mirrors the transcriptional defects observed in the fast Pol II mutant. Furthermore, AFF4 knockdown leads to increased AFF1 levels at chromatin, and vice versa. In summary, our data demonstrate that AFF1 and AFF4 function, to some extent, antagonistically to ensure proper Pol II transcription.
Overall design Genome binding/occupancy profiling by high throughput sequencing. CSTF2 ChIP-seq in WT, AFF4 MT and AFF4 KO serum-induced HCT116 cells.
Contributor(s) Lin C, Liu X
Citation(s) 37528066
Submission date Feb 07, 2023
Last update date Jun 05, 2024
Contact name Xiaoxu Liu
Organization name Southeast University
Department Institute of Life Sciences
Lab the Key Laboratory of Developmental Genes and Human Disease
Street address 2 Sipailou
City Nanjing
State/province Jiangsu
ZIP/Postal code 210018
Country China
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (3)
GSM7031292 HCT116_WT-CSTF2+Serum
GSM7031293 HCT116_AFF4 MT-CSTF2+Serum
GSM7031294 HCT116_AFF4 KO-CSTF2+Serum
This SubSeries is part of SuperSeries:
GSE207813 Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation
BioProject PRJNA932347

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Supplementary file Size Download File type/resource
GSE224753_RAW.tar 604.8 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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