Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

Bentsen, Mette; Goymann, Philipp; Schultheis, Hendrik; Petrova, Anastasiia; Klee, Kathrin; Fust, Annika; Preussner, Jens; Kuenne, Carsten; Braun, Thomas; Kim, Johnny; Looso, Mario

doi:10.1101/869560

Cited by 8 publications

(11 citation statements)

References 86 publications

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“…To further assess which transcription factors might be involved in gene expression control, we carried out footprinting analysis on differential accessible regions from our ATAC-seq datasets (Fig. 3B; Bentsen et al, 2019). In differential accessible regions, motifs for KLF (e.g.…”

Section: Resultsmentioning

confidence: 99%

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Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma

Rogerson

Ogden

Britton

et al. 2020

Preprint

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Oesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths and yet compared to other common cancers, we know relatively little about the underlying molecular mechanisms. Barrett's oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the specific events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies of BO and OAC and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin in OAC cells to directly regulate cell cycle genes specifically in OAC. Our findings have potential prognostic significance as the survival of patients with high expression of KLF5 target genes is significantly lower. We have provided new insights into the gene expression networks in OAC and the mechanisms behind progression to OAC, chiefly the repurposing of KLF5 for novel regulatory activity in OAC. similar GO terms to those enriched in genes upregulated in OAC compared to BO ( Fig. 3F).GSEA also identified the same gene set terms: "G2M checkpoint" and "E2F1 targets" (Fig. 3G).Next we asked whether these genes are directly regulated by KLF5, and carried out ChIPseq for KLF5 in OE19 cells. Anti-KLF5 antibodies precipitated KLF5 ( Supplementary Fig. 3I) and biological replicates were highly reproducible ( Supplementary Fig. 3J). Therefore, we took the overlap of peaks between biological replicates forward for downstream analyses, resulting in 13,542 peaks ( Supplementary Fig. 3K; Supplementary Table S5). These peaks are highly enriched in the KLF5 motif, demonstrating the validity of the dataset, and also in AP1(FRA1) and GATA (GATA6) motifs, which we have previously revealed in genome wide studies as implicated in OAC (Britton et al., 2017; Rogerson et al., 2019) ( Supplementary Fig. 3L). Focussing on the 97 genes that are upregulated in OAC and also downregulated after KLF5 depletion, 97% have a KLF5 ChIP-seq peak within 0.5 Mb of the TSS and the median distance between a KLF5 ChIP-seq peak and the TSS was 15,604 bp ( Supplementary Fig. 3M). This is indicative of direct regulation by KLF5. An example gene is CDC25B which harbours multiple KLF5 ChIP-seq peaks surrounding its locus (Fig. 3H).Collectively, these results suggest a direct activator role of KLF5 in controlling cell cycle genes in OAC. The KLF5 cistrome is reconfigured during the progression from BO to OAC.Having determined a role for KLF5 in controlling cell cycle associated gene expression in OAC cells, we sought to determine the mechanism through which KLF5 acquires these functions. We first asked whether KLF5 expression changes in the transition from BO to OAC, however no increase in expression was found (Fig. 4A). An alternative me...

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Section: Resultsmentioning

confidence: 99%

“…To analyse footprinting signatures in ATAC-seq data the TOBIAS package was used (v0.5.1; Bentsen et al, 2019; available at https://github.molgen.mpg.de/loosolab/TOBIAS). Merged BAM files from each condition were processed using ATACorrect, footprint scores calculated using FootprintScores and differential footprinting analysis using BINDetect.…”

Section: Methodsmentioning

confidence: 99%

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma

Rogerson

Ogden

Britton

et al. 2020

Preprint

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“…Peaks were called using MACS2 [56]. TF footprinting was performed with TOBIAS [57] based on the aligned reads, peaks and TF motifs from JASPAR (JASPAR 2020 non-redundant vertebrate CORE PFMs) [58]. TOBIAS performs Tn5 bias correction, generates footprint scores for each base within the peaks, scans for TFBSs using the given TF motifs, and finally classifies each TFBS as bound or unbound based on the footprint scores.…”

Section: Methodsmentioning

confidence: 99%

Comparative regulomics reveals pervasive selection on gene dosage following whole genome duplication

Gillard

Groenvold

Roesaeg

et al. 2020

Preprint

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Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago. We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Although ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards pseudogenization, strong evolutionary constraints have frequently also favoured symmetric shifts in gene dosage of both copies, likely to achieve gene dose reduction while avoiding accumulation of toxic mutations. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one source of novel binding sites driving tissue-specific gains expression. Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

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“…S3B). To identify transcription factors whose occupancy was modified, we carried out in silico footprinting analyses of the differentially accessible regions at the proximal promoter 27 and Ins2, but also Gcg or Sst and sometimes all three was seen along with intermediate cells in clusters 1 and 4, with cluster 4 cells trans-differentiating to an alpha and perhaps also delta cell identity ( Fig. 6C and Fig.…”

Section: Taf4 Regulated Gene Expression Programs In Beta Cellsmentioning

confidence: 99%

The TFIID subunit Taf4 is required for pancreatic beta cell function and identity

Kleiber

Davidson

Mengus

et al. 2020

Preprint

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We selectively inactivated the Taf4 subunit of general transcription factor TFIID in adult murine pancreatic beta cells (BCs). Taf4 inactivation rapidly diminishes expression of critical genes involved in BC function leading to increased glycaemia, lowered blood insulin levels, defective glucose-stimulated insulin secretion and in the longer term reduced BC mass through apoptosis of a subpopulation of BCs. Nevertheless, glycaemia and blood insulin levels are stabilised after 11 weeks with mutant animals showing long term survival. Bulk RNA-seq and ATAC-seq and single cell RNA-seq on isolated Langerhans islets show that Taf4 loss leads to major remodelling of chromatin accessibility and gene expression not only in targeted BCs, but also alpha and delta cells. One week after Taf4-loss cells with mixed BC, alpha and/or delta cell identities were observed as well as a BC population transdifferentiating into alpha cells. Trans-differentiation was associated with the combinatorial action of the Mafb, Mafg, Bptf and Foxp1 transcription factors. Taf4 is therefore essential for BC function and identity and we identify a novel set of factors associated with BC transdifferentiation.3 Introduction.

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Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

Cited by 8 publications

References 86 publications

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma

Comparative regulomics reveals pervasive selection on gene dosage following whole genome duplication

The TFIID subunit Taf4 is required for pancreatic beta cell function and identity

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