GEO series

YY1 is a structural regulator of enhancer-promoter loops [HiChIP]

GSE99519 Homo sapiens (human) Other 17 samples Submitted 2017/11/16 Platform GPL17021Platform GPL16791

At a glance

human · 17 samples

Organism: Homo sapiens (human)
Samples: 17 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein.

Read the full summary ↓

Here we show that the transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements in all cells examined. YY1 forms dimers that can facilitate DNA interactions. Deletion of YY1 binding sites or depletion of YY1 can disrupt enhancer-promoter looping and normal gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.

This dataset

Open GSE99519 in finder → Find more datasets →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE99519_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA388695 and SRA study SRP108380. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 29224777) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 17 more — browse all 17 samples with per-sample file links →

Datasets on a similar topic

GSE97179 Single Cell Methylome Signatures Reveal Distinct Neuronal Populations and Regulatory Elements in the Mammalian Cortex 6172 samples shares regulator
GSE282636 Multiplex generation and single cell analysis of structural variants in mammalian genomes 197 samples shares structural
GSE290623 Opposing functions of distinct regulatory T cell subsets in colorectal cancer 142 samples shares regulator
GSE256246 Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function. 132 samples shares regulator
GSE234699 SMYD5 is a regulator of the mild hypothermia response 127 samples shares regulator
GSE286473 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry 95 samples shares regulator
GSE296242 Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions 81 samples shares enhancer-promoter
GSE292300 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: ChIP-seq 76 samples shares regulator

Search all datasets in GEO →

Share this dataset

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.