NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE207320 Query DataSets for GSE207320
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 1]
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
 
Contributor(s) Lin C, Liu X
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jul 01, 2022
Last update date Jul 03, 2023
Contact name Xiaoxu Liu
E-mail(s) liuxiaoxu1010@126.com
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 (2)
GSM6284521 A549_AFF1 shRNA_AFF4
GSM6284522 A549_AFF1 shRNA-1_Pol II
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
Relations
BioProject PRJNA854802

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
GSE207320_RAW.tar 272.5 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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