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Series GSE169465 Query DataSets for GSE169465
Status Public on Jul 05, 2022
Title G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The DSIF complex, which is composed of the Supt4h and Supt5h transcription elongation proteins, clamps RNA polymerase II (RNAPII) onto DNA templates—facilitating polymerase processivity. Lowering of DSIF components can differentially decrease expression of certain neurodegenerative disease-gene alleles containing nucleotide repeat expansions, suggesting that DSIF assists RNAPII progression through these alleles. To identify sequence features that globally affect the actions of DSIF in neuronal cells, we used ultra—deep ChIP-seq analyses together with RNA-seq to investigate and quantify the genome-wide consequences of reducing DSIF on template occupancy and transcription by RNAPII. Our ChIP-seq analysis yielded an average of 378 million reads per sample, facilitating precision in identification of read end-points. The results indicate that DSIF is differentially utilized throughout the human genome by RNAPII in its occupancy of human DNA and that the G+C_composition of the template segment being transcribed determines the extent to which the polymerase relies on DSIF for template occupancy. Additional analysis by us of previously published data obtained. We following knockdown of the Supt5h component of DSIF in murine fibroblasts showed similar effects. We further observed that DSIF reduction resulted in progressively decreased RNAPII occupancy of template during transcript elongation in genes of high G+C content, but had little effect on genes low in G+C content. Our discovery that DSIF dependency varies in different template regions according to G+C content and transcript length suggest a biochemical basis for selective effects of deficiency of DSIF components on genes containing expansions of G+C-rich nucleotide repeats.
 
Overall design Compare elongating RNAPII's DNA occupancy by ChIP-seq and RNA transcription by RNA-seq when Supt4 is present or absent in human neuronal progenitor cells
 
Contributor(s) Deng N, Zhang Y
Citation(s) 35910045
Submission date Mar 23, 2021
Last update date Aug 03, 2022
Contact name Stanley N. Cohen
E-mail(s) sncohen@stanford.edu
Organization name Stanford University
Department Genetics
Street address 300 Pasteur Drive, Lane Bldg, Rm L-314
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (2)
GSM5203715 GM23225_NPC_unt
GSM5203717 GM23225_NPC_Supt4-kd
This SubSeries is part of SuperSeries:
GSE169466 G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II
Relations
BioProject PRJNA716749
SRA SRP312005

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Supplementary file Size Download File type/resource
GSE169465_summary_gene_FPKM_table.txt.gz 159.9 Kb (ftp)(http) TXT
GSE169465_summary_gene_count_table.txt.gz 145.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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