bims-crepig 2022-01-30 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2022‒01‒30
eighteen papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit

Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response.
Single-cell ATAC-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition.
Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections.
A natural product targets BRD4 to inhibit phase separation and gene transcription.
MYC amplifies gene expression through global changes in transcription factor dynamics.
Brahma safeguards canalization of cardiac mesoderm differentiation.
SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers.
Selective translation of epigenetic modifiers affects the temporal pattern and differentiation of neural stem cells.
Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development.
Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution.
SOX2 mediates metabolic reprogramming of prostate cancer cells.
Sin3a drives mesenchymal-to-epithelial transition through cooperating with Tet1 in somatic cell reprogramming.
A genetic compensatory mechanism regulated by Jun and Mef2d modulates the expression of distinct class IIa Hdacs to ensure peripheral nerve myelination and repair.
scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells.
DNA-induced spatial entrapment of general transcription machinery can stabilize gene expression in a nondividing cell.
Tumor suppressor CEBPA interacts with and inhibits DNMT3A activity.
YTHDF2 promotes multiple myeloma cell proliferation via STAT5A/MAP2K2/p-ERK axis.
Canonical TGFβ signaling induces collective invasion in colorectal carcinogenesis through a Snail1- and Zeb1-independent partial EMT.

Mol Cell. 2022 Jan 20. pii: S1097-2765(21)01140-0. [Epub ahead of print]

Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response.

Jackson A Hoffman, Kevin W Trotter, Christopher R Day, James M Ward, Kaoru Inoue, Joseph Rodriguez, Trevor K Archer.

  The hormone-stimulated glucocorticoid receptor (GR) modulates transcription by interacting with thousands of enhancers and GR binding sites (GBSs) throughout the genome. Here, we examined the effects of GR binding on enhancer dynamics and investigated the contributions of individual GBSs to the hormone response. Hormone treatment resulted in genome-wide reorganization of the enhancer landscape in breast cancer cells. Upstream of the DDIT4 oncogene, GR bound to four sites constituting a hormone-dependent super enhancer. Three GBSs were required as hormone-dependent enhancers that differentially promoted histone acetylation, transcription frequency, and burst size. Conversely, the fourth site suppressed transcription and hormone treatment alleviated this suppression. GR binding within the super enhancer promoted a loop-switching mechanism that allowed interaction of the DDIT4 TSS with the active GBSs. The unique functions of each GR binding site contribute to hormone-induced transcriptional heterogeneity and demonstrate the potential for targeted modulation of oncogene expression.

Keywords:  4C-seq; ATAC-seq; chromatin; eRNA; enhancer; glucocorticoid receptor; histone acetylation; nuclear receptor; super enhancer; transcription

DOI:  https://doi.org/10.1016/j.molcel.2021.12.035
Cell Rep. 2022 Jan 25. pii: S2211-1247(21)01809-X. [Epub ahead of print]38(4): 110294

Single-cell ATAC-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition.

Connor Finkbeiner, Isabel Ortuño-Lizarán, Akshayalakshmi Sridhar, Marcus Hooper, Sidnee Petter, Thomas A Reh.

  We previously used single-cell transcriptomic analysis to characterize human fetal retinal development and assessed the degree to which retinal organoids recapitulate normal development. We now extend the transcriptomic analyses to incorporate single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), a powerful method used to characterize potential gene regulatory networks through the changes in accessible chromatin that accompany cell-state changes. The combination of scATAC-seq and single-cell RNA sequencing (scRNA-seq) provides a view of developing human retina at an unprecedented resolution. We identify key transcription factors relevant to specific fates and the order of the transcription factor cascades that define each of the major retinal cell types. The changing chromatin landscape is largely recapitulated in retinal organoids; however, there are differences in Notch signaling and amacrine cell gene regulation. The datasets we generated constitute an excellent resource for the continued improvement of retinal organoid technology and have the potential to inform and accelerate regenerative medicine approaches to retinal diseases.

Keywords:  chromatin; development; epigenetics; gene regulation

DOI:  https://doi.org/10.1016/j.celrep.2021.110294
Nat Commun. 2022 Jan 24. 13(1): 463

Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections.

Xinyu Xiang, Yu Tao, Jonathan DiRusso, Fei-Man Hsu, Jinchun Zhang, Ziwei Xue, Julien Pontis, Didier Trono, Wanlu Liu, Amander T Clark.

Germ cells are essential to pass DNA from one generation to the next. In human reproduction, germ cell development begins with the specification of primordial germ cells (PGCs) and a failure to specify PGCs leads to human infertility. Recent studies have revealed that the transcription factor network required for PGC specification has diverged in mammals, and this has a significant impact on our understanding of human reproduction. Here, we reveal that the Hominidae-specific Transposable Elements (TEs) LTR5Hs, may serve as TEENhancers (TE Embedded eNhancers) to facilitate PGC specification. LTR5Hs TEENhancers become transcriptionally active during PGC specification both in vivo and in vitro with epigenetic reprogramming leading to increased chromatin accessibility, localized DNA demethylation, enrichment of H3K27ac, and occupation of key hPGC transcription factors. Inactivation of LTR5Hs TEENhancers with KRAB mediated CRISPRi has a significant impact on germ cell specification. In summary, our data reveals the essential role of Hominidae-specific LTR5Hs TEENhancers in human germ cell development.

DOI: https://doi.org/10.1038/s41467-022-28105-1
iScience. 2022 Jan 21. 25(1): 103719

A natural product targets BRD4 to inhibit phase separation and gene transcription.

Cong Wang, Huasong Lu, Xiangzhong Liu, Xiang Gao, Wenjing Tian, Haifeng Chen, Yuhua Xue, Qiang Zhou.

  The BET-bromodomain protein BRD4 uses two bromodomains to target acetyl-histones and other domains to recruit P-TEFb and other transcription factors to stimulate transcription of proto-oncogenes and key cell identity genes. Recent studies show that its ability to form phase-separated condensates that cluster preferentially at the super-enhancer regions of target genes is key for BRD4 to exert its functions. Here, we describe the identification of a natural product called PCG from polygonum cuspidatum Sieb.et Zucc., a traditional Chinese medicinal herb, that directly binds to BRD4. This binding inhibits BRD4 phase separation, turns dynamic BRD4 nuclear condensates into static aggregates, and effectively shuts down transcription of BRD4-dependent genes. Thus, through PCG we have discovered a BET inhibitor that not only selectively targets BRD4 but also works by suppressing phase separation, a mechanism of action that is different from those of the other known BET inhibitors.

Keywords:  Biological sciences; Molecular biology; Natural product biochemistry

DOI:  https://doi.org/10.1016/j.isci.2021.103719
Cell Rep. 2022 Jan 25. pii: S2211-1247(21)01807-6. [Epub ahead of print]38(4): 110292

MYC amplifies gene expression through global changes in transcription factor dynamics.

Simona Patange, David A Ball, Yihan Wan, Tatiana S Karpova, Michelle Girvan, David Levens, Daniel R Larson.

  The MYC oncogene has been studied for decades, yet there is still intense debate over how this transcription factor controls gene expression. Here, we seek to answer these questions with an in vivo readout of discrete events of gene expression in single cells. We engineered an optogenetic variant of MYC (Pi-MYC) and combined this tool with single-molecule RNA and protein imaging techniques to investigate the role of MYC in modulating transcriptional bursting and transcription factor binding dynamics in human cells. We find that the immediate consequence of MYC overexpression is an increase in the duration rather than in the frequency of bursts, a functional role that is different from the majority of human transcription factors. We further propose that the mechanism by which MYC exerts global effects on the active period of genes is by altering the binding dynamics of transcription factors involved in RNA polymerase II complex assembly and productive elongation.

Keywords:  MYC; single-molecule imaging; transcription

DOI:  https://doi.org/10.1016/j.celrep.2021.110292
Nature. 2022 Jan 26.

Brahma safeguards canalization of cardiac mesoderm differentiation.

Swetansu K Hota, Kavitha S Rao, Andrew P Blair, Ali Khalilimeybodi, Kevin M Hu, Reuben Thomas, Kevin So, Vasumathi Kameswaran, Jiewei Xu, Benjamin J Polacco, Ravi V Desai, Nilanjana Chatterjee, Austin Hsu, Jonathon M Muncie, Aaron M Blotnick, Sarah A B Winchester, Leor S Weinberger, Ruth Hüttenhain, Irfan S Kathiriya, Nevan J Krogan, Jeffrey J Saucerman, Benoit G Bruneau.

Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization1,2. Canalization is essential for stabilizing cell fate, but the mechanisms that underlie robust canalization are unclear. Here we show that the BRG1/BRM-associated factor (BAF) chromatin-remodelling complex ATPase gene Brm safeguards cell identity during directed cardiogenesis of mouse embryonic stem cells. Despite the establishment of a well-differentiated precardiac mesoderm, Brm-/- cells predominantly became neural precursors, violating germ layer assignment. Trajectory inference showed a sudden acquisition of a non-mesodermal identity in Brm-/- cells. Mechanistically, the loss of Brm prevented de novo accessibility of primed cardiac enhancers while increasing the expression of neurogenic factor POU3F1, preventing the binding of the neural suppressor REST and shifting the composition of BRG1 complexes. The identity switch caused by the Brm mutation was overcome by increasing BMP4 levels during mesoderm induction. Mathematical modelling supports these observations and demonstrates that Brm deletion affects cell fate trajectory by modifying saddle-node bifurcations2. In the mouse embryo, Brm deletion exacerbated mesoderm-deleted Brg1-mutant phenotypes, severely compromising cardiogenesis, and reveals an in vivo role for Brm. Our results show that Brm is a compensable safeguard of the fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory.

DOI: https://doi.org/10.1038/s41586-021-04336-y
Mol Cell. 2022 Jan 17. pii: S1097-2765(21)01142-4. [Epub ahead of print]

SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers.

Amandine Barral, Gabrielle Pozo, Lucas Ducrot, Giorgio L Papadopoulos, Sandrine Sauzet, Andrew J Oldfield, Giacomo Cavalli, Jérôme Déjardin.

  Gene silencing by heterochromatin plays a crucial role in cell identity. Here, we characterize the localization, the biogenesis, and the function of an atypical heterochromatin, which is simultaneously enriched in the typical H3K9me3 mark and in H3K36me3, a histone mark usually associated with gene expression. We identified thousands of dual regions in mouse embryonic stem (ES) cells that rely on the histone methyltransferases SET domain bifurcated 1 (SETDB1) and nuclear set domain (NSD)-containing proteins to generate H3K9me3 and H3K36me3, respectively. Upon SETDB1 removal, dual domains lose both marks, gain signatures of active enhancers, and come into contact with upregulated genes, suggesting that it might be an important pathway by which genes are controlled by heterochromatin. In differentiated tissues, a subset of these dual domains is destabilized and becomes enriched in active enhancer marks, providing a mechanistic insight into the involvement of heterochromatin in the maintenance of cell identity.

Keywords:  cellular identity; enhancer; gene expression; heterochromatin

DOI:  https://doi.org/10.1016/j.molcel.2021.12.037
Nat Commun. 2022 Jan 25. 13(1): 470

Selective translation of epigenetic modifiers affects the temporal pattern and differentiation of neural stem cells.

Quan Wu, Yuichi Shichino, Takaya Abe, Taeko Suetsugu, Ayaka Omori, Hiroshi Kiyonari, Shintaro Iwasaki, Fumio Matsuzaki.

The cerebral cortex is formed by diverse neurons generated sequentially from neural stem cells (NSCs). A clock mechanism has been suggested to underlie the temporal progression of NSCs, which is mainly defined by the transcriptome and the epigenetic state. However, what drives such a developmental clock remains elusive. We show that translational control of histone H3 trimethylation in Lys27 (H3K27me3) modifiers is part of this clock. We find that depletion of Fbl, an rRNA methyltransferase, reduces translation of both Ezh2 methyltransferase and Kdm6b demethylase of H3K27me3 and delays the progression of the NSC state. These defects are partially phenocopied by simultaneous inhibition of H3K27me3 methyltransferase and demethylase, indicating the role of Fbl in the genome-wide H3K27me3 pattern. Therefore, we propose that Fbl drives the intrinsic clock through the translational enhancement of the H3K27me3 modifiers that predominantly define the NSC state.

DOI: https://doi.org/10.1038/s41467-022-28097-y
Nat Commun. 2022 Jan 24. 13(1): 457

Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development.

Margaret E Magaletta, Macrina Lobo, Eric M Kernfeld, Hananeh Aliee, Jack D Huey, Teagan J Parsons, Fabian J Theis, René Maehr.

Maldevelopment of the pharyngeal endoderm, an embryonic tissue critical for patterning of the pharyngeal region and ensuing organogenesis, ultimately contributes to several classes of human developmental syndromes and disorders. Such syndromes are characterized by a spectrum of phenotypes that currently cannot be fully explained by known mutations or genetic variants due to gaps in characterization of critical drivers of normal and dysfunctional development. Despite the disease-relevance of pharyngeal endoderm, we still lack a comprehensive and integrative view of the molecular basis and gene regulatory networks driving pharyngeal endoderm development. To close this gap, we apply transcriptomic and chromatin accessibility single-cell sequencing technologies to generate a multi-omic developmental resource spanning pharyngeal endoderm patterning to the emergence of organ-specific epithelia in the developing mouse embryo. We identify cell-type specific gene regulation, distill GRN models that define developing organ domains, and characterize the role of an immunodeficiency-associated forkhead box transcription factor.

DOI: https://doi.org/10.1038/s41467-022-28067-4
Genome Biol. 2022 Jan 24. 23(1): 34

Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution.

Jingya Yuan, Haojie Sun, Yijin Wang, Lulu Li, Shiting Chen, Wu Jiao, Guanghong Jia, Longfei Wang, Junrong Mao, Zhongfu Ni, Xiue Wang, Qingxin Song.

  BACKGROUND: Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their interactions shape chromatin structure and gene expression in wheat. The open chromatin enrichment and network Hi-C (OCEAN-C) is a powerful antibody-independent method to detect chromatin interactions between open chromatin regions throughout the genome.RESULTS: Here we generate open chromatin interaction maps for hexaploid wheat and its tetraploid and diploid relatives using OCEAN-C. The anchors of chromatin loops show high chromatin accessibility and are concomitant with several active histone modifications, with 67% of them interacting with multiple loci. Binding motifs of various transcription factors are significantly enriched in the hubs of open chromatin interactions (HOCIs). The genes linked by HOCIs represent higher expression level and lower coefficient expression variance than the genes linked by other loops, which suggests HOCIs may coordinate co-expression of linked genes. Thousands of interchromosomal loops are identified, while limited interchromosomal loops (0.4%) are identified between homoeologous genes in hexaploid wheat. Moreover, we find structure variations contribute to chromatin interaction divergence of homoeologs and chromatin topology changes between different wheat species. The genes with discrepant chromatin interactions show expression alteration in hexaploid wheat compared with its tetraploid and diploid relatives.
CONCLUSIONS: Our results reveal open chromatin interactions in different wheat species, which provide new insights into the role of open chromatin interactions in gene expression during the evolution of polyploid wheat.

Keywords:  Evolution; OCEAN-C; Open chromatin interaction; Polyploidy; Wheat

DOI:  https://doi.org/10.1186/s13059-022-02611-3
Oncogene. 2022 Jan 24.

SOX2 mediates metabolic reprogramming of prostate cancer cells.

Larischa de Wet, Anthony Williams, Marc Gillard, Steven Kregel, Sophia Lamperis, Lisa C Gutgesell, Jordan E Vellky, Ryan Brown, Kelly Conger, Gladell P Paner, Heng Wang, Elizabeth E Platz, Angelo M De Marzo, Ping Mu, Jonathan L Coloff, Russell Z Szmulewitz, Donald J Vander Griend.

New strategies are needed to predict and overcome metastatic progression and therapy resistance in prostate cancer. One potential clinical target is the stem cell transcription factor SOX2, which has a critical role in prostate development and cancer. We thus investigated the impact of SOX2 expression on patient outcomes and its function within prostate cancer cells. Analyses of SOX2 expression among a case-control cohort of 1028 annotated tumor specimens demonstrated that SOX2 expression confers a more rapid time to metastasis and decreased patient survival after biochemical recurrence. SOX2 ChIP-Seq analyses revealed SOX2-binding sites within prostate cancer cells which differ significantly from canonical embryonic SOX2 gene targets, and prostate-specific SOX2 gene targets are associated with multiple oncogenic pathways. Interestingly, phenotypic and gene expression analyses after CRISPR-mediated deletion of SOX2 in castration-resistant prostate cancer cells, as well as ectopic SOX2 expression in androgen-sensitive prostate cancer cells, demonstrated that SOX2 promotes changes in multiple metabolic pathways and metabolites. SOX2 expression in prostate cancer cell lines confers increased glycolysis and glycolytic capacity, as well as increased basal and maximal oxidative respiration and increased spare respiratory capacity. Further, SOX2 expression was associated with increased quantities of mitochondria, and metabolomic analyses revealed SOX2-associated changes in the metabolism of purines, pyrimidines, amino acids and sugars, and the pentose phosphate pathway. Analyses of SOX2 gene targets with central functions metabolism (CERK, ECHS1, HS6SDT1, LPCAT4, PFKP, SLC16A3, SLC46A1, and TST) document significant expression correlation with SOX2 among RNA-Seq datasets derived from patient tumors and metastases. These data support a key role for SOX2 in metabolic reprogramming of prostate cancer cells and reveal new mechanisms to understand how SOX2 enables metastatic progression, lineage plasticity, and therapy resistance. Further, our data suggest clinical opportunities to exploit SOX2 as a biomarker for staging and imaging, as well as a potential pharmacologic target.

DOI: https://doi.org/10.1038/s41388-021-02157-x
Stem Cell Res Ther. 2022 Jan 24. 13(1): 29

Sin3a drives mesenchymal-to-epithelial transition through cooperating with Tet1 in somatic cell reprogramming.

Jiabao Feng, Fugui Zhu, Dan Ye, Qingquan Zhang, Xudong Guo, Changsheng Du, Jiuhong Kang.

  BACKGROUND: Identifying novel regulatory factors and uncovered mechanisms of somatic cell reprogramming will be helpful for basic research and clinical application of induced pluripotent stem cells (iPSCs). Sin3a, a multifunctional transcription regulator, has been proven to be involved in the maintenance of pluripotency in embryonic stem cells (ESCs), but the role of Sin3a in somatic cell reprogramming remains unclear.METHODS: RNA interference of Sin3a during somatic cell reprogramming was realized by short hairpin RNAs. Reprogramming efficiency was evaluated by the number of alkaline phosphatase (AP)-positive colonies and Oct4-GFP-positive colonies. RNA sequencing was performed to identify the influenced biological processes after Sin3a knockdown and further confirmed by quantitative RT-PCR (qRT-PCR), western blotting and flow cytometry. The interaction between Sin3a and Tet1 was detected by coimmunoprecipitation. The enrichment of Sin3a and Tet1 at the epithelial gene promoters was measured by chromatin immunoprecipitation. Furthermore, DNA methylation patterns at the gene loci were investigated by hydroxymethylated DNA immunoprecipitation. Finally, Sin3a mutants that disrupt the interaction of Sin3a and Tet1 were also introduced to assess the importance of the Sin3a-Tet1 interaction during the mesenchymal-to-epithelial transition (MET) process.
RESULTS: We found that Sin3a was gradually increased during OSKM-induced reprogramming and that knockdown of Sin3a significantly impaired MET at the early stage of reprogramming and iPSC generation. Mechanistic studies showed that Sin3a recruited Tet1 to facilitate the hydroxymethylation of epithelial gene promoters. Moreover, disrupting the interaction of Sin3a and Tet1 significantly blocked MET and iPSC generation.
CONCLUSIONS: Our studies revealed that Sin3a was a novel mediator of MET during early reprogramming, where Sin3a functioned as an epigenetic coactivator, cooperating with Tet1 to activate the epithelial program and promote the initiation of somatic cell reprogramming. These findings highlight the importance of Sin3a in the MET process and deepen our understanding of the epigenetic regulatory network of early reprogramming.

Keywords:  Hydroxymethylation; Mesenchymal-to-epithelial transition; Reprogramming; Sin3a; Tet1

DOI:  https://doi.org/10.1186/s13287-022-02707-4
Elife. 2022 Jan 25. pii: e72917. [Epub ahead of print]11

A genetic compensatory mechanism regulated by Jun and Mef2d modulates the expression of distinct class IIa Hdacs to ensure peripheral nerve myelination and repair.

Sergio Velasco-Aviles, Nikiben Patel, Angeles Casillas-Bajo, Laura Frutos-Rincón, Enrique Velasco-Serna, Juana Gallar, Peter Arthur-Farraj, Jose A Gomez-Sanchez, Hugo Cabedo.

  The class IIa histone deacetylases (HDACs) have pivotal roles in the development of different tissues. Of this family, Schwann cells express Hdac4, 5 and 7 but not Hdac9. Here we show that a transcription factor regulated genetic compensatory mechanism within this family of proteins, blocks negative regulators of myelination ensuring peripheral nerve developmental myelination and remyelination after injury. Thus, when Hdac4 and 5 are knocked-out from Schwann cells in mice, a JUN-dependent mechanism induces the compensatory overexpression of Hdac7 permitting, although with a delay, the formation of the myelin sheath. When Hdac4,5 and 7 are simultaneously removed, the Myocyte-specific enhancer-factor d (MEF2D) binds to the promoter and induces the de novo expression of Hdac9, and although several melanocytic lineage genes are misexpressed and Remak bundle structure is disrupted, myelination proceeds after a long delay. Thus, our data unveil a finely tuned compensatory mechanism within the class IIa Hdac family, coordinated by distinct transcription factors, that guarantees the ability of Schwann cells to myelinate during development and remyelinate after nerve injury.

Keywords:  cell biology; mouse; neuroscience; rat

DOI:  https://doi.org/10.7554/eLife.72917
Mol Cell. 2022 Jan 17. pii: S1097-2765(21)01143-6. [Epub ahead of print]

scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells.

Matthew Tegowski, Mathieu N Flamand, Kate D Meyer.

N6-methyladenosine (m6A) is an abundant RNA modification that plays critical roles in RNA regulation and cellular function. Global m6A profiling has revealed important aspects of m6A distribution and function, but to date such studies have been restricted to large populations of cells. Here, we develop a method to identify m6A sites transcriptome-wide in single cells. We uncover surprising heterogeneity in the presence and abundance of m6A sites across individual cells and identify differentially methylated mRNAs across the cell cycle. Additionally, we show that cellular subpopulations can be distinguished based on their RNA methylation signatures, independent from gene expression. These studies reveal fundamental features of m6A that have been missed by m6A profiling of bulk cells and suggest the presence of cell-intrinsic mechanisms for m6A deposition.

DOI: https://doi.org/10.1016/j.molcel.2021.12.038
Proc Natl Acad Sci U S A. 2022 Jan 25. pii: e2116091119. [Epub ahead of print]119(4):

DNA-induced spatial entrapment of general transcription machinery can stabilize gene expression in a nondividing cell.

Khayam Javed, Jerome Jullien, Gaurav Agarwal, Nicola Lawrence, Richard Butler, Pantelis Savvas Ioannou, Farhat Nazir, J B Gurdon.

  An important characteristic of cell differentiation is its stability. Only rarely do cells or their stem cell progenitors change their differentiation pathway. If they do, it is often accompanied by a malfunction such as cancer. A mechanistic understanding of the stability of differentiated states would allow better prospects of alleviating the malfunctioning. However, such complete information is yet elusive. Earlier experiments performed in Xenopus oocytes to address this question suggest that a cell may maintain its gene expression by prolonged binding of cell type-specific transcription factors. Here, using DNA competition experiments, we show that the stability of gene expression in a nondividing cell could be caused by the local entrapment of part of the general transcription machinery in transcriptionally active regions. Strikingly, we found that transcriptionally active and silent forms of the same DNA template can stably coexist within the same nucleus. Both DNA templates are associated with the gene-specific transcription factor Ascl1, the core factor TBP2, and the polymerase II (Pol-II) ser5 C-terminal domain (CTD) phosphorylated form, while Pol-II ser2 CTD phosphorylation is restricted to the transcriptionally dominant template. We discover that the active and silent DNA forms are physically separated in the oocyte nucleus through partition into liquid-liquid phase-separated condensates. Altogether, our study proposes a mechanism of transcriptional regulation involving a spatial entrapment of general transcription machinery components to stabilize the active form of a gene in a nondividing cell.

Keywords:  Ascl1; Xenopus oocyte; liquid–liquid phase separation; stable gene expression; transcriptional regulation

DOI:  https://doi.org/10.1073/pnas.2116091119
Sci Adv. 2022 Jan 28. 8(4): eabl5220

Tumor suppressor CEBPA interacts with and inhibits DNMT3A activity.

Xiufei Chen, Wenjie Zhou, Ren-Hua Song, Shuang Liu, Shu Wang, Yujia Chen, Chao Gao, Chenxi He, Jianxiong Xiao, Lei Zhang, Tianxiang Wang, Peng Liu, Kunlong Duan, Zhouli Cheng, Chen Zhang, Jinye Zhang, Yiping Sun, Felix Jackson, Fei Lan, Yun Liu, Yanhui Xu, Justin Jong-Leong Wong, Pu Wang, Hui Yang, Yue Xiong, Tong Chen, Yan Li, Dan Ye.

DNA methyltransferases (DNMTs) catalyze DNA methylation, and their functions in mammalian embryonic development and diseases including cancer have been extensively studied. However, regulation of DNMTs remains under study. Here, we show that CCAAT/enhancer binding protein α (CEBPA) interacts with the long splice isoform DNMT3A, but not the short isoform DNMT3A2. CEBPA, by interacting with DNMT3A N-terminus, blocks DNMT3A from accessing DNA substrate and thereby inhibits its activity. Recurrent tumor-associated CEBPA mutations, such as preleukemic CEBPAN321D mutation, which is particularly potent in causing AML with high mortality, disrupt DNMT3A association and cause aberrant DNA methylation, notably hypermethylation of PRC2 target genes. Consequently, leukemia cells with the CEBPAN321D mutation are hypersensitive to hypomethylation agents. Our results provide insights into the functional difference between DNMT3A isoforms and the regulation of de novo DNA methylation at specific loci in the genome. Our study also suggests a therapeutic strategy for the treatment of CEBPA-mutated leukemia with DNA-hypomethylating agents.

DOI: https://doi.org/10.1126/sciadv.abl5220
Oncogene. 2022 Jan 24.

YTHDF2 promotes multiple myeloma cell proliferation via STAT5A/MAP2K2/p-ERK axis.

Zhen Hua, Rongfang Wei, Mengjie Guo, Zigen Lin, Xichao Yu, Xinying Li, Chunyan Gu, Ye Yang.

Multiple myeloma (MM) is still incurable partially due to lacking effective therapeutic targets. Aberrant N6-methyladenosine (m6A) RNA modification plays a vital role in many cancers, however few researches are executed in MM. We first screened the m6A-related genes in MM patient cohorts and correlated these genes with patient outcomes. We found that YTHDF2, a well-recognized m6A reader, was increased in MM patients and associated with poor outcomes. Decreased YTHDF2 expression hampered MM cell proliferation in vitro and in vivo, while enforced YTHDF2 expression reversed those effects. The analyses of m6A-RIP-seq and RIP-PCR indicated that STAT5A was the downstream target of YTHDF2, which was binding to the m6A modification site of STAT5A to promote its mRNA degradation. ChIP-seq and PCR assays revealed that STAT5A suppressed MM cell proliferation by occupying the transcription site of MAP2K2 to decrease ERK phosphorylation. In addition, we confirmed that YTHDF2 mediated the unphosphorylated form of STAT5A to inhibit the expression of MAP2K2/p-ERK. In conclusion, our study highlights that YTHDF2/STAT5A/MAP2K2/p-ERK axis plays a key role in MM proliferation and targeting YTHDF2 may be a promising therapeutic strategy.

DOI: https://doi.org/10.1038/s41388-022-02191-3
Oncogene. 2022 Jan 24.

Canonical TGFβ signaling induces collective invasion in colorectal carcinogenesis through a Snail1- and Zeb1-independent partial EMT.

Marion Flum, Severin Dicks, Yu-Hsiang Teng, Monika Schrempp, Alexander Nyström, Melanie Boerries, Andreas Hecht.

Local invasion is the initial step towards metastasis, the main cause of cancer mortality. In human colorectal cancer (CRC), malignant cells predominantly invade as cohesive collectives and may undergo partial epithelial-mesenchymal transition (pEMT) at the invasive front. How this particular mode of stromal infiltration is generated is unknown. Here we investigated the impact of oncogenic transformation and the microenvironment on tumor cell invasion using genetically engineered organoids as CRC models. We found that inactivation of the Apc tumor suppressor combined with expression of oncogenic KrasG12D and dominant-negative Trp53R172H did not cell-autonomously induce invasion in vitro. However, oncogenic transformation primed organoids for activation of a collective invasion program upon exposure to the prototypical microenvironmental factor TGFβ1. Execution of this program co-depended on a permissive extracellular matrix which was further actively remodeled by invading organoids. Although organoids shed some epithelial properties particularly at the invasive edge, TGFβ1-stimulated organoids largely maintained epithelial gene expression while additionally implementing a mesenchymal transcription pattern, resulting in a pEMT phenotype that did not progress to a fully mesenchymal state. Notably, while TGFβ1 induced pEMT and promoted collective invasion, it abrogated self-renewal capacity of TKA organoids which correlated with the downregulation of intestinal stem cell (ISC) marker genes. Mechanistically, induction of the non-progressive pEMT required canonical TGFβ signaling mediated by Smad transcription factors (TFs), whereas the EMT master regulators Snail1 and Zeb1 were dispensable. Gene expression profiling provided further evidence for pEMT of TGFβ1-treated organoids and showed that their transcriptomes resemble those of human poor prognosis CMS4 cancers which likewise exhibit pEMT features. We propose that collective invasion in colorectal carcinogenesis is triggered by microenvironmental stimuli through activation of a novel, transcription-mediated form of non-progressive pEMT independently of classical EMT regulators.

DOI: https://doi.org/10.1038/s41388-022-02190-4