A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation

Donohue, Laura K.; Guo, Margaret; Zhao, Yang; Jung, Namyoung; Bussat, Rose T.; Kim, Daniel S.; Neela, Poornima H.; Kellman, Laura N.; Garcia, Omar S.; Meyers, Robin M.; Altman, Russ B.; Khavari, Paul A.

doi:10.1016/j.xgen.2022.100191

Cited by 8 publications

(5 citation statements)

References 127 publications

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“…To infer candidate direct targets of these TFs in astrocytes we overlapped putative TF binding sites based on their known motifs with transcription start site (TSS) proximal regions of open chromatin in astrocytes. This was done for two independent ATAC‐seq datasets (Donohue et al, 2022 ; M. Song et al, 2019 ). Based on the analysis, 28 TFs are putatively directly targeted by NFIA and/or NFIB using the Song et al data and are also upregulated (2.1‐fold enrichment, p = .0002) in ABS9‐iAs in comparison to ZS9‐iAs, which lack NFIA/B in their cassette.…”

Section: Resultsmentioning

confidence: 99%

Section: Distinct Astrocytic Features Were Associated With Specific T...mentioning

confidence: 99%

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Transcription factor combinations that define human astrocyte identity encode significant variation of maturity and function

Baranes

Hastings

Rahman

et al. 2023

Glia

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Increasing evidence indicates that cellular identity can be reduced to the distinct gene regulatory networks controlled by transcription factors (TFs). However, redundancy exists in these states as different combinations of TFs can induce broadly similar cell types. We previously demonstrated that by overcoming gene silencing, it is possible to deterministically reprogram human pluripotent stem cells directly into cell types of various lineages. In the present study we leverage the consistency and precision of our approach to explore four different TF combinations encoding astrocyte identity, based on previously published reports. Analysis of the resulting induced astrocytes (iAs) demonstrated that all four cassettes generate cells with the typical morphology of in vitro astrocytes, which expressed astrocyte-specific markers. The transcriptional profiles of all four iAs clustered tightly together and displayed similarities with mature human astrocytes, although maturity levels differed between cells. Importantly, we found that the TF cassettes induced iAs with distinct differences with regards to their cytokine response and calcium signaling. In vivo transplantation of selected iAs into immunocompromised rat brains demonstrated long term stability and integration. In conclusion, all four TF combinations were able to induce stable astrocyte-like cells that were morphologically similar but showed subtle differences with respect to their transcriptome. These subtle differences translated into distinct differences with regards to cell function, that could be related to maturation state and/or regional identity of the resulting cells. This insight opens an opportunity to precision-engineer cells to meet functional requirements, for example, in the context of therapeutic cell transplantation.

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Section: Resultsmentioning

confidence: 99%

Section: Distinct Astrocytic Features Were Associated With Specific T...mentioning

confidence: 99%

Transcription factor combinations that define human astrocyte identity encode significant variation of maturity and function

Baranes

Hastings

Rahman

et al. 2023

Glia

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“…To further investigate a three-dimensional structure of XP33-LCE2 cluster in keratinocytes, we simultaneously assessed the expression of XP33 , chromatin accessibility and chromatin looping in LCE2 locus across 15 types of epithelial cells including keratinocytes using publicly available data from a recent study [ 34 ]. As expected, XP33 was found expressed only in keratinocytes but not in any other epithelial cell types analysed (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…All the data used in the study are available on GEO NCBI: RNA-seq of human keratinocytes after p63 knock-down (GSE67382) [ 31 ], scRNA-seq of human skin (GSE202352) [ 43 ], RNA-seq and ChIP-seq for H3K27ac, p63, and Pol2 in human keratinocytes differentiated in vitro (GSE59827) [ 44 ], ChIP-seq for CTCF and SMC1A in differentiated human keratinocytes (GSE84657) [ 33 ], RNA-seq, ATAC-seq and H3K27ac-HiChIP of epithelia (GSE188405) [ 34 ], RNA-seq and ChIP-seq for H3K27ac and p63 in human fibroblasts (GSE126390) [ 29 ], ChIP-seq for ZNF750 and KLF4 in differentiated human keratinocytes (GSE57702) [ 36 ]. ChIP-seq for H3K27ac and CTCF across different cell types were downloaded from ENCODE Project [ 45 ].…”

Section: Methodsmentioning

confidence: 99%

Epigenetic priming of an epithelial enhancer by p63 and CTCF controls expression of a skin-restricted gene XP33

Smirnov,

Lena,

Tosetti

et al. 2023

Cell Death Discov.

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The transcription factor p63 is a renowned master regulator of gene expression of stratified epithelia. While multiple proteins have been identified as p63 bona fide targets, little is known about non-coding RNAs (ncRNAs) whose transcription is controlled by p63. Here, we describe a skin-specific non-coding RNA XP33 as a novel target of p63. XP33 levels are increased during keratinocyte differentiation in vitro, while its depletion results in decreased expression of late cornified gene LCE2D. By using publicly available multi-omics data, we show that CTCF and p63 establish an epithelial enhancer to prime XP33 transcription in a tissue-restricted manner. XP33 promoter and enhancer form a chromatin loop exclusively in keratinocytes but not in other cell types. Moreover, the XP33 enhancer is occupied by differentiation-specific factors that control XP33 transcription. Altogether, we identify a tissue-specific non-coding RNA whose expression is epigenetically regulated by p63 and CTCF.

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“…5E) (Lopez-Pajares et al, 2015;Napoli et al, 2024). Regulatory elements with cell-specific activities appear to utilize different combinations of co-enriching motifs alongside p63 (Donohue et al, 2022). The extent to which p63 amplification or other transcription factor availability drives differential p63-dependent activities at gene regulatory elements, both during development and disease, requires more investigation to unravel.…”

Section: Discussionmentioning

confidence: 99%

Context dependent activity of p63-bound gene regulatory elements

McCann,

Baniulyte,

Woodstock

et al. 2024

Preprint

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The p53 family of transcription factors regulate numerous organismal processes including the development of skin and limbs, ciliogenesis, and preservation of genetic integrity and tumor suppression. p53 family members control these processes and gene expression networks through engagement with DNA sequences within gene regulatory elements. Whereas p53 binding to its cognate recognition sequence is strongly associated with transcriptional activation, p63 can mediate both activation and repression. How the DNA sequence of p63-bound gene regulatory elements is linked to these varied activities is not yet understood. Here, we use massively parallel reporter assays (MPRA) in a range of cellular and genetic contexts to investigate the influence of DNA sequence on p63-mediated transcription. Most regulatory elements with a p63 response element motif (p63RE) activate transcription, with those sites bound by p63 more frequently or adhering closer to canonical p53 family response element sequences driving higher transcriptional output. The most active regulatory elements are those also capable of binding p53. Elements uniquely bound by p63 have varied activity, with p63RE-mediated repression associated with lower overall GC content in flanking sequences. Comparison of activity across cell lines suggests differential activity of elements may be regulated by a combination of p63 abundance or context-specific cofactors. Finally, changes in p63 isoform expression dramatically alters regulatory element activity, primarily shifting inactive elements towards a strong p63-dependent activity. Our analysis of p63-bound gene regulatory elements provides new insight into how sequence, cellular context, and other transcription factors influence p63-dependent transcription. These studies provide a framework for understanding how p63 genomic binding locally regulates transcription. Additionally, these results can be extended to investigate the influence of sequence content, genomic context, chromatin structure on the interplay between p63 isoforms and p53 family paralogs.

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A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation

Cited by 8 publications

References 127 publications

Transcription factor combinations that define human astrocyte identity encode significant variation of maturity and function

Transcription factor combinations that define human astrocyte identity encode significant variation of maturity and function

Epigenetic priming of an epithelial enhancer by p63 and CTCF controls expression of a skin-restricted gene XP33

Context dependent activity of p63-bound gene regulatory elements

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