Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB

Lemma, Roza Berhanu; Ledsaak, Marit; Fuglerud, Bettina M.; Sandve, Geir Kjetil; Eskeland, Ragnhild; Gabrielsen, Odd S.

doi:10.1038/s41598-021-88516-w

Cited by 13 publications

(18 citation statements)

References 83 publications

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“…A de novo motif discovery analysis of the 500 bp centered on inaccessible FOXA1 or HNF4A binding sites revealed strong enrichment for each TF’s motif, but no other strong signals. Similarly, we found no evidence for enrichment of predicted K562 PFs AP1 (FOS/JUN; MA0099.2; Biddie et al, 2011 ), GATA1 (MA0035.4; Iwafuchi-Doi and Zaret, 2014 ), MYB (MA0100.1; Lemma et al, 2021 ), or SPI1 (PU.1; MA0080.1; Iwafuchi-Doi and Zaret, 2014 ) either in inaccessible binding sites over randomly chosen sites or in HNF4A over FOXA1 binding sites ( Figure 3—figure supplement 2 ). Thus, the similar activities of FOXA1 and HNF4A are not explained by pioneering activity provided by endogenous K562 TFs.…”

Section: Resultsmentioning

confidence: 70%

A test of the pioneer factor hypothesis using ectopic liver gene activation

Hansen

Loell

Cohen

2022

eLife

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The Pioneer Factor Hypothesis (PFH) states that pioneer factors (PFs) are a subclass of transcription factors (TFs) that bind to and open inaccessible sites and then recruit non-pioneer factors (nonPFs) that activate batteries of silent genes. The PFH predicts that ectopic gene activation requires the sequential activity of qualitatively different TFs. We tested the PFH by expressing the endodermal PF FOXA1 and nonPF HNF4A in K562 lymphoblast cells. While co-expression of FOXA1 and HNF4A activated a burst of endoderm-specific gene expression, we found no evidence for a functional distinction between these two TFs. When expressed independently, both TFs bound and opened inaccessible sites, activated endodermal genes, and 'pioneered' for each other, although FOXA1 required fewer copies of its motif for binding. A subset of targets required both TFs, but the predominant mode of action at these targets did not conform to the sequential activity predicted by the PFH. From these results we hypothesize an alternative to the PFH where 'pioneer activity' depends not on categorically different TFs but rather on the affinity of interaction between TF and DNA.

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Section: Resultsmentioning

confidence: 70%

A test of the pioneer factor hypothesis using ectopic liver gene activation

Hansen

Loell

Cohen

2022

eLife

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“…6d ), which relate to cell growth 41 and hematological cell fate 42,43 . CUT&Tag also detected TFBMs not captured by ENCODE H3K27ac, such as those for Elk1, Elk4 and ETS, which are transcription factors involved in hematopoiesis 44 in line with the K562 lineage (lymphoblast), and this was observed when calling peaks with both SEACR and MACS2 ( Supplementary Fig. 7 ).…”

Section: Resultsmentioning

confidence: 95%

CUT&Tag recovers up to half of ENCODE ChIP-seq peaks in modifications of H3K27

Abbasova

Schilder

et al. 2022

Preprint

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Techniques for genome-wide epigenetic profiling have been undergoing rapid development toward recovery of high quality data from bulk and single cell samples. DNA-protein interactions have traditionally been profiled via chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq), which has become the gold standard for studying histone modifications or transcription factor binding. Cleavage Under Targets & Tagmentation (CUT&Tag) is a promising new technique, which enables profiling of such interactions in situ at high sensitivity and is adaptable to single cell applications. However thorough evaluation and benchmarking against established ChIP-seq datasets are still lacking. Here we comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Across a total of 30 new and 6 published CUT&Tag datasets we found that no experiment recovers more than 50% of known ENCODE peaks, regardless of the histone mark. We tested peak callers MACS2 and SEACR, identifying optimal peak calling parameters. Balancing both precision and recall of known ENCODE peaks, SEACR without retention of duplicates showed the best performance. We found that reducing PCR cycles during library preparation lowered duplication rates at the expense of ENCODE peak recovery. Despite the moderate ENCODE peak recovery, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments and will facilitate future efforts to apply CUT&Tag in human tissues and single cells.

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“…Additional K-562-specific ChIP-Seq peak data for MYB were sourced from the GEO (GSE124541) database. The original peak calling pipeline (21) was employed using the hg38 reference genome. Further GFI1B data for K-562 cells were retrieved from the GEO (GSE117944) database (22) and lifted over to hg38.…”

Section: Methodsmentioning

confidence: 99%

Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs

Minaeva,

Domingo,

Rentzsch

et al. 2024

Preprint

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Understanding the role of transcription and transcription factors in cellular identity and disease, such as cancer and autoimmunity, is essential. However, comprehensive data resources for cell line-specific transcription factor-to-target gene annotations are currently limited. To address this, we developed a straightforward method to define regulons that capture the cell-specific aspects of TF binding and transcript expression levels. By integrating cellular transcriptome and transcription factor binding data, we generated regulons for four common cell lines comprising both proximal and distal cell line-specific regulatory events. Through systematic benchmarking involving transcription factor knockout experiments, we demonstrated performance on par with state-of-the-art methods, with our method being easily applicable to other cell types of interest. We present case studies using three cancer single-cell datasets to showcase the utility of these cell-type-specific regulons in exploring transcriptional dysregulation. In summary, this study provides a valuable tool and a resource for systematically exploring cell line-specific transcriptional regulations, emphasizing the utility of network analysis in deciphering disease mechanisms.

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Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB

Cited by 13 publications

References 83 publications

A test of the pioneer factor hypothesis using ectopic liver gene activation

A test of the pioneer factor hypothesis using ectopic liver gene activation

CUT&Tag recovers up to half of ENCODE ChIP-seq peaks in modifications of H3K27

Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs

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