Transcription imparts architecture, function, and logic to enhancer units

Tippens, Nathaniel D.; Liang, Jin; Leung, King Y; Ozer, Abdullah; Booth, James G.; Lis, John T.; Yu, Haiyuan

doi:10.1101/818849

Cited by 17 publications

(29 citation statements)

References 56 publications

(76 reference statements)

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“…The cell type-specific binding of GR demonstrates that information beyond the GBS directs its binding, so we used motif searching to identify other factors that may associate with GORs. Our search was limited to +/- 150 bp from the summit of GR binding, as this distance captures the regulatory information between two core promoters that are associated with candidate enhancers (Core, Martins, et al 2014; Scruggs et al 2015; Tippens et al 2020). Motifs for FOXA, CEBP, and AP-1 (which consists of a heterodimer of FOS, JUN, and ATF family members, or c-JUN homodimers) were enriched in A549-specific GORs, as compared to U2OS-specific GORs (Table S3).…”

Section: Resultsmentioning

confidence: 99%

“…Only 3% of CCREs with repressed transcription are GR-bound (Figure 5A). PRO-seq profiles of CCREs generally show a bidirectional pattern of transcription, with TF motifs between the two transcription start sites (Core, Martins, et al 2014; Tippens et al 2020). We examined the PRO-seq signal at GORs with and without induced CCREs in A549 and U2OS cells (Figure 5B, C).…”

Section: Resultsmentioning

confidence: 99%

“…These eRNAs can be detected with high sensitivity by sequencing nascent RNAs because they produce bidirectional transcripts, similar to promoters (Andersson, Gebhard, et al 2014; Core, Martins, et al 2014; Scruggs et al 2015; Mikhaylichenko et al 2018; Wissink et al 2019). The architecture of promoters and enhancers are similar, as TFs bind in the nucleosome-depleted region between the two core promoters for both types of elements (Core, Martins, et al 2014; Andersson, Sandelin, Danko 2015; Tome et al 2018; Tippens et al 2020), and the specific TFs bound likely distinguish enhancers from promoters (Andersson, Sandelin 2020).…”

Section: Introductionmentioning

confidence: 99%

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Glucocorticoid receptor collaborates with pioneer factors and AP-1 to execute genome-wide regulation

Wissink

Ehmsen

et al. 2021

Preprint

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The glucocorticoid receptor (GR) regulates transcription through binding to specific DNA motifs, particularly at enhancers. While the motif to which it binds is constant across cell types, GR has cell type-specific binding at genomic loci, resulting in regulation of different genes. The presence of other bound transcription factors (TFs) is hypothesized to strongly influence where GR binds. Here, we addressed the roles of other TFs in the glucocorticoid response by comparing changes in GR binding and nascent transcription at promoters and distal candidate cis-regulatory elements (CCREs) in two distinct human cancer cell types. We found that after glucocorticoid treatment, GR binds to thousands of genomic loci that are primarily outside of promoter regions and are potentially enhancers. The majority of these GR binding sites are cell-type specific, and they are associated with pioneer factor binding. A small fraction of GR occupied regions (GORs) displayed increased bidirectional nascent transcription, which is a characteristic of many active enhancers, after glucocorticoid treatment. Non-promoter GORs with increased transcription were specifically enriched for AP-1 binding prior to glucocorticoid treatment. These results support a model of transcriptional regulation in which multiple classes of TFs are required. The pioneer factors increase chromatin accessibility, facilitating the binding of GR and additional factors. AP-1 binding poises a fraction of accessible sites to be rapidly transcribed upon glucocorticoid-induced GR binding. The coordinated activity of multiple TFs then results in cell type-specific changes in gene expression. We anticipate that many models of inducible gene expression also require multiple distinct TFs that act at multiple steps of transcriptional regulation.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Glucocorticoid receptor collaborates with pioneer factors and AP-1 to execute genome-wide regulation

Wissink

Ehmsen

et al. 2021

Preprint

Self Cite

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“…TFs and co-factors binding to DNA enhancer regions recruit RNA polymerase II, leading to the covalent modification of flanking histone tails (including H3K27ac and H3K4me3) and to the bi-directional transcription of enhancer RNA (eRNA) (Heinz et al, 2015;Krijger and de Laat, 2016;Rothschild and Basu, 2017). As an emerging class of non-coding RNA, eRNA is widespread at all active enhancers in quantities that are proportional to enhancer activity (Core et al, 2014;Tippens et al, 2020). Rather than merely being by-products of enhancer activity, several lines of evidence suggest that some, if not all, eRNAs are functional (Catarino and Stark, 2018;Gu et al, 2018;Hou and Kraus).…”

Section: Introductionmentioning

confidence: 99%

Population-level variation of enhancer expression identifies novel disease mechanisms in the human brain

Dong

Hoffman

Apontes

et al. 2021

Preprint

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Enhancer RNAs (eRNAs) constitute an important tissue- and cell-type-specific layer of the regulome. Identification of risk variants for neuropsychiatric diseases within enhancers underscores the importance of understanding the population-level variation of eRNAs in the human brain. We jointly analyzed cell type-specific transcriptome and regulome data to identify 30,795 neuronal and 23,265 non-neuronal eRNAs, expanding the catalog of known human brain eRNAs by an order of magnitude. Examination of the population-level variation of the transcriptome and regulome in 1,382 brain samples identified reproducible changes affecting cis- and trans-co-regulation of eRNA-gene modules in schizophrenia. We show that 13% of schizophrenia heritability is jointly mediated in cis by brain gene and eRNA expression. Inclusion of eRNAs in transcriptome-wide association studies facilitated fine-mapping and functional interpretation of disease loci. Overall, our study characterizes the eRNA-gene regulome and genetic mechanisms in the human cortex in both healthy and disease states.

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“…We designed a pair of pegRNAs encoding a 185-bp deletion at FMR1 that removes this repeat-expansion region. The e-NMU region corresponds to a recently discovered enhancer for NMU , experimentally verified using Cas9/paired-gRNA deletions 6,17 . We designed a pair of pegRNAs encoding a 710-bp deletion to delete this enhancer.…”

Section: Resultsmentioning

confidence: 89%

Precise genomic deletions using paired prime editing

Choi

Chen

Suiter

et al. 2021

Preprint

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Technologies that precisely delete genomic sequences in a programmed fashion can be used to study function as well as potentially for gene therapy. The leading contemporary method for programmed deletion uses CRISPR/Cas9 and pairs of guide RNAs (gRNAs) to generate two nearby double-strand breaks, which is often followed by deletion of the intervening sequence during DNA repair. However, this approach can be inefficient and imprecise, with errors including small indels at the two target sites as well as unintended large deletions and more complex rearrangements. Here we describe a prime editing-based method that we term PRIME-Del, which induces a deletion using a pair of prime editing gRNAs (pegRNAs) that target opposite DNA strands, effectively programming not only the sites that are nicked but also the outcome of the repair. We demonstrate that PRIME-Del achieves markedly higher precision in programming deletions than CRISPR/Cas9 and gRNA pairs. We also show that PRIME-Del can be used to couple genomic deletions with short insertions, enabling deletions whose junctions do not fall at protospacer-adjacent motif (PAM) sites. Finally, we demonstrate that lengthening the time window of expression of prime editing components can substantially enhance efficiency without compromising precision. We anticipate that PRIME-Del will be broadly useful in enabling precise, flexible programming of genomic deletions, including in-frame deletions, as well as for epitope tagging and potentially for programming rearrangements.

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Transcription imparts architecture, function, and logic to enhancer units

Cited by 17 publications

References 56 publications

Glucocorticoid receptor collaborates with pioneer factors and AP-1 to execute genome-wide regulation

Glucocorticoid receptor collaborates with pioneer factors and AP-1 to execute genome-wide regulation

Population-level variation of enhancer expression identifies novel disease mechanisms in the human brain

Precise genomic deletions using paired prime editing

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