bims-crepig 2023-03-26 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023–03–26
eight papers selected by
Connor Rogerson, University of Cambridge

Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks.
Enhancers display constrained sequence flexibility and context-specific modulation of motif function.
Super-enhancer-associated transcription factors collaboratively regulate trophoblast-active gene expression programs in human trophoblast stem cells.
Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis.
Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion.
Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention.
Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation.
The molecular consequences of androgen activity in the human breast.

Oncogene. 2023 Mar 22.

Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks.

Hélène Neyret-Kahn, Jacqueline Fontugne, Xiang Yu Meng, Clarice S Groeneveld, Luc Cabel, Tao Ye, Elodie Guyon, Clémentine Krucker, Florent Dufour, Elodie Chapeaublanc, Audrey Rapinat, Daniel Jeffery, Laura Tanguy, Victoria Dixon, Yann Neuzillet, Thierry Lebret, David Gentien, Irwin Davidson, Yves Allory, Isabelle Bernard-Pierrot, François Radvanyi.

Muscle-invasive bladder cancer (BLCA) is an aggressive disease. Consensus BLCA transcriptomic subtypes have been proposed, with two major Luminal and Basal subgroups, presenting distinct molecular and clinical characteristics. However, how these distinct subtypes are regulated remains unclear. We hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of BLCA subtypes. Through integrated RNA-sequencing and epigenomic profiling of histone marks in primary tumours, cancer cell lines, and normal human urothelia, we established the first integrated epigenetic map of BLCA and demonstrated the link between subtype and epigenetic control. We identified the repertoire of activated super-enhancers and highlighted Basal, Luminal and Normal-associated SEs. We revealed super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal subgroups including FOXA1 and ZBED2, respectively. FOXA1 CRISPR-Cas9 mutation triggered a shift from Luminal to Basal phenotype, confirming its role in Luminal identity regulation and induced ZBED2 overexpression. In parallel, we showed that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in cancer cells through STAT2 inhibition. Our study furthers the understanding of epigenetic regulation of muscle-invasive BLCA and identifies a co-regulated network of super-enhancers and associated transcription factors providing potential targets for the treatment of this aggressive disease.

DOI: https://doi.org/10.1038/s41388-023-02662-1
Genome Res. 2023 Mar 20.

Enhancers display constrained sequence flexibility and context-specific modulation of motif function.

Franziska Reiter, Bernardo P de Almeida, Alexander Stark.

The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding sites (motifs) for different transcription factors (TFs). Most of the research on enhancer sequences has been focused on TF motif presence, whereas the enhancer syntax, that is, the flexibility of important motif positions and how the sequence context modulates the activity of TF motifs, remains poorly understood. Here, we explore the rules of enhancer syntax by a two-pronged approach in Drosophila melanogaster S2 cells: we (1) replace important TF motifs by all possible 65,536 eight-nucleotide-long sequences and (2) paste eight important TF motif types into 763 positions within 496 enhancers. These complementary strategies reveal that enhancers display constrained sequence flexibility and the context-specific modulation of motif function. Important motifs can be functionally replaced by hundreds of sequences constituting several distinct motif types, but these are only a fraction of all possible sequences and motif types. Moreover, TF motifs contribute with different intrinsic strengths that are strongly modulated by the enhancer sequence context (the flanking sequence, the presence and diversity of other motif types, and the distance between motifs), such that not all motif types can work in all positions. The context-specific modulation of motif function is also a hallmark of human enhancers, as we demonstrate experimentally. Overall, these two general principles of enhancer sequences are important to understand and predict enhancer function during development, evolution, and in disease.

DOI: https://doi.org/10.1101/gr.277246.122
Nucleic Acids Res. 2023 Mar 23. pii: gkad215. [Epub ahead of print]

Super-enhancer-associated transcription factors collaboratively regulate trophoblast-active gene expression programs in human trophoblast stem cells.

Mijeong Kim, Enoch Appiah Adu-Gyamfi, Jonghwan Kim, Bum-Kyu Lee.

The placenta is an essential organ that supports the growth and development of the fetus during pregnancy. However, cell type-specific enhancers and transcription factors (TFs), and the mechanisms underlying the maintenance and differentiation of trophoblast stem cell (TSC) populations in the human placenta remain elusive. Here, using human TSCs as a model system, we identify 31,362 enhancers that are enriched with the motifs of previously reported TSC-pivotal TFs, including TEAD4, GATA2/3 and TFAP2C. Subsequently, we identify 580 super-enhancers (SEs) and 549 SE-associated genes. These genes are robustly expressed in the human placenta and include numerous TFs, implying that SE-associated TFs (SE-TFs) may play crucial roles in placental development. Additionally, we identify the global binding sites of five TSC-pivotal SE-TFs (FOS, GATA2, MAFK, TEAD4 and TFAP2C), revealing that they preferentially co-occupy enhancers, regulate each other and form a trophoblast-active gene regulatory network. Loss-of-function studies unveil that the five TFs promote self-renewal of TSCs by activating proliferation-associated genes while repressing developmental genes. We further reveal that the five TFs exert conserved and unique functions on placental development between humans and mice. Our study provides important insights into the roles of human TSC-pivotal TFs in regulating placenta-specific gene expression programs.

DOI: https://doi.org/10.1093/nar/gkad215
Nat Struct Mol Biol. 2023 Mar 20.

Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis.

Dounia Djeghloul, Andrew Dimond, Sherry Cheriyamkunnel, Holger Kramer, Bhavik Patel, Karen Brown, Alex Montoya, Chad Whilding, Yi-Fang Wang, Matthias E Futschik, Nicolas Veland, Thomas Montavon, Thomas Jenuwein, Matthias Merkenschlager, Amanda G Fisher.

Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and polycomb repressor complexes, binds to chromosomes throughout mitosis and their depletion results in increased chromosome size. In the present study, we show that enzymes that catalyze H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly, however, mutants lacking histone 3 lysine 9 trimethylation (H3K9me3) have unusually small and compact mitotic chromosomes associated with increased histone H3 phospho Ser10 (H3S10ph) and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous first protein lysine methyltransferase Suv39h1 or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wild-type versus Suv39h1/Suv39h2 double-null mouse embryonic stem cells revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.

DOI: https://doi.org/10.1038/s41594-023-00943-7
Mol Cell. 2023 Mar 15. pii: S1097-2765(23)00153-3. [Epub ahead of print]

Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion.

Elena Battistello, Kimberlee A Hixon, Dawn E Comstock, Clayton K Collings, Xufeng Chen, Javier Rodriguez Hernaez, Soobeom Lee, Kasey S Cervantes, Madeline M Hinkley, Konstantinos Ntatsoulis, Annamaria Cesarano, Kathryn Hockemeyer, W Nicholas Haining, Matthew T Witkowski, Jun Qi, Aristotelis Tsirigos, Fabiana Perna, Iannis Aifantis, Cigall Kadoch.

  Highly coordinated changes in gene expression underlie T cell activation and exhaustion. However, the mechanisms by which such programs are regulated and how these may be targeted for therapeutic benefit remain poorly understood. Here, we comprehensively profile the genomic occupancy of mSWI/SNF chromatin remodeling complexes throughout acute and chronic T cell stimulation, finding that stepwise changes in localization over transcription factor binding sites direct site-specific chromatin accessibility and gene activation leading to distinct phenotypes. Notably, perturbation of mSWI/SNF complexes using genetic and clinically relevant chemical strategies enhances the persistence of T cells with attenuated exhaustion hallmarks and increased memory features in vitro and in vivo. Finally, pharmacologic mSWI/SNF inhibition improves CAR-T expansion and results in improved anti-tumor control in vivo. These findings reveal the central role of mSWI/SNF complexes in the coordination of T cell activation and exhaustion and nominate small-molecule-based strategies for the improvement of current immunotherapy protocols.

Keywords:  ATP-dependent chromatin remodeling; CRISPR screening; CUT&Tag; HNF1B; PROTACs; SWI/SNF; T cells; immunotherapy; small-molecule inhibitors; transcription factors

DOI:  https://doi.org/10.1016/j.molcel.2023.02.026
Genome Biol. 2023 Mar 22. 24(1): 53

Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention.

Fahad Ullah, Saira Jabeen, Maayan Salton, Anireddy S N Reddy, Asa Ben-Hur.

   BACKGROUND: Alternative splicing is a widespread regulatory phenomenon that enables a single gene to produce multiple transcripts. Among the different types of alternative splicing, intron retention is one of the least explored despite its high prevalence in both plants and animals. The recent discovery that the majority of splicing is co-transcriptional has led to the finding that chromatin state affects alternative splicing. Therefore, it is plausible that transcription factors can regulate splicing outcomes.
RESULTS: We provide evidence for the hypothesis that transcription factors are involved in the regulation of intron retention by studying regions of open chromatin in retained and excised introns. Using deep learning models designed to distinguish between regions of open chromatin in retained introns and non-retained introns, we identified motifs enriched in IR events with significant hits to known human transcription factors. Our model predicts that the majority of transcription factors that affect intron retention come from the zinc finger family. We demonstrate the validity of these predictions using ChIP-seq data for multiple zinc finger transcription factors and find strong over-representation for their peaks in intron retention events.
CONCLUSIONS: This work opens up opportunities for further studies that elucidate the mechanisms by which transcription factors affect intron retention and other forms of splicing.
AVAILABILITY: Source code available at https://github.com/fahadahaf/chromir.

Keywords:  Alternative splicing; Deep learning; Intron retention

DOI:  https://doi.org/10.1186/s13059-023-02885-1
BMC Bioinformatics. 2023 Mar 20. 24(1): 102

Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation.

Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl A Keller, Elisabeth F Heuston, Stacie M Anderson, Martha Kirby, David Bodine, Yu Zhang, Ross C Hardison.

   BACKGROUND: Epigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to identify the regulatory events controlling cell differentiation.
RESULTS: To reduce the complexity, we developed a package, called Snapshot, for clustering and visualizing candidate cis-regulatory elements (cCREs) based on their epigenetic signals during cell differentiation. This package first introduces a binarized indexing strategy for clustering the cCREs. It then provides a series of easily interpretable figures for visualizing the signal and epigenetic state patterns of the cCREs clusters during the cell differentiation. It can also use different hierarchies of cell types to highlight the epigenetic history specific to any particular cell lineage. We demonstrate the utility of Snapshot using data from a consortium project for ValIdated Systematic IntegratiON (VISION) of epigenomic data in hematopoiesis.
CONCLUSION: The package Snapshot can identify all distinct clusters of genomic locations with unique epigenetic signal patterns during cell differentiation. It outperforms other methods in terms of interpreting and reproducing the identified cCREs clusters. The package of Snapshot is available at GitHub: https://github.com/guanjue/Snapshot .

Keywords:  Cell differentiation; Epigenetic state visualization; cCRE Clustering and Visualization; cCRE indexing

DOI:  https://doi.org/10.1186/s12859-023-05223-1
Cell Genom. 2023 Mar 08. 3(3): 100272

The molecular consequences of androgen activity in the human breast.

Florian Raths, Mehran Karimzadeh, Nathan Ing, Andrew Martinez, Yoona Yang, Ying Qu, Tian-Yu Lee, Brianna Mulligan, Suzanne Devkota, Wayne T Tilley, Theresa E Hickey, Bo Wang, Armando E Giuliano, Shikha Bose, Hani Goodarzi, Edward C Ray, Xiaojiang Cui, Simon R V Knott.

  Estrogen and progesterone have been extensively studied in the mammary gland, but the molecular effects of androgen remain largely unexplored. Transgender men are recorded as female at birth but identify as male and may undergo gender-affirming androgen therapy to align their physical characteristics and gender identity. Here we perform single-cell-resolution transcriptome, chromatin, and spatial profiling of breast tissues from transgender men following androgen therapy. We find canonical androgen receptor gene targets are upregulated in cells expressing the androgen receptor and that paracrine signaling likely drives sex-relevant androgenic effects in other cell types. We also observe involution of the epithelium and a spatial reconfiguration of immune, fibroblast, and vascular cells, and identify a gene regulatory network associated with androgen-induced fat loss. This work elucidates the molecular consequences of androgen activity in the human breast at single-cell resolution.

Keywords:  androgen regulation of human breast homeostasis; breast microenvironment; cellular metabolism; chromatin regulation; hormone receptor; lactation; multiplexed immunohistochemistry by co-detection by indexing; single-cell ATAC sequencing; single-cell RNA sequencing; transcriptional control

DOI:  https://doi.org/10.1016/j.xgen.2023.100272