GEO series

The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [RNA-seq]

GSE188415 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2024/11/06 Platform GPL11154Platform GPL24247Platform GPL24676

At a glance

RNA-seq (gene expression) · mouse · 26 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 26 samples: 9 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation.

Read the full summary ↓

Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.

This dataset

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Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE188415_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA778754 and SRA study SRP345064. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 conditions, mostly in triplicate

control for PAF1 data RNA-seq ×6 PNUTS KO RNA-seq ×3 LEO1 KO RNA-seq ×3 Paf1 WT RNA-seq ×3 Paf1 cKO RNA-seq ×3 control for PAF1 data CCRF-CEM RNA-seq ×2 shPAF1 CCRF-CEM RNA-seq ×2 control for PAF1 data HEL RNA-seq ×2 +1 more

Supports a between-group comparison across 26 samples.

How we read this: 9 replicated groups read from 26 sample titles; they account for 26 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM5681050 control for PAF1 data RNA-seq rep1 control for PAF1 data R…
GSM5681051 control for PAF1 data RNA-seq rep2 control for PAF1 data R…
GSM5681052 control for PAF1 data RNA-seq rep3 control for PAF1 data R…
GSM5681053 PNUTS KO RNA-seq rep1 PNUTS KO RNA-seq
GSM5681054 PNUTS KO RNA-seq rep2 PNUTS KO RNA-seq
GSM5681055 PNUTS KO RNA-seq rep3 PNUTS KO RNA-seq
GSM5681056 control for PAF1 data RNA-seq rep4 control for PAF1 data R…
GSM5681057 control for PAF1 data RNA-seq rep5 control for PAF1 data R…
GSM5681058 control for PAF1 data RNA-seq rep6 control for PAF1 data R…
GSM5681059 LEO1 KO RNA-seq rep1 LEO1 KO RNA-seq
GSM5681060 LEO1 KO RNA-seq rep2 LEO1 KO RNA-seq
GSM5681061 LEO1 KO RNA-seq rep3 LEO1 KO RNA-seq
GSM5681062 control for PAF1 data CCRF-CEM RNA-seq rep1 control for PAF1 data C…
GSM5681063 control for PAF1 data CCRF-CEM RNA-seq rep2 control for PAF1 data C…
GSM5681064 shPAF1 CCRF-CEM RNA-seq rep1 shPAF1 CCRF-CEM RNA-seq
GSM5681065 shPAF1 CCRF-CEM RNA-seq rep2 shPAF1 CCRF-CEM RNA-seq
GSM5681066 control for PAF1 data HEL RNA-seq rep1 control for PAF1 data H…
GSM5681067 control for PAF1 data HEL RNA-seq rep2 control for PAF1 data H…
GSM5681068 shPAF1 HEL RNA-seq rep1 shPAF1 HEL RNA-seq
GSM5681069 shPAF1 HEL RNA-seq rep2 shPAF1 HEL RNA-seq
GSM5681070 Paf1 WT RNA-seq rep1 Paf1 WT RNA-seq
GSM5681071 Paf1 WT RNA-seq rep2 Paf1 WT RNA-seq
GSM5681072 Paf1 WT RNA-seq rep3 Paf1 WT RNA-seq
GSM5681073 Paf1 cKO RNA-seq rep1 Paf1 cKO RNA-seq
GSM5681074 Paf1 cKO RNA-seq rep2 Paf1 cKO RNA-seq
GSM5681075 Paf1 cKO RNA-seq rep3 Paf1 cKO RNA-seq

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.