bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2021–11–21
thirty-one papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Relaxed 3D genome conformation facilitates the pluripotent to totipotent-like state transition in embryonic stem cells.
  2. Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors.
  3. A single-cell atlas of chromatin accessibility in the human genome.
  4. Genome-wide mapping of G-quadruplex structures with CUT&Tag.
  5. High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq).
  6. A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals.
  7. Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones.
  8. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina.
  9. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.
  10. Genome surveillance by HUSH-mediated silencing of intronless mobile elements.
  11. MMP-9 drives the melanomagenic transcription program through histone H3 tail proteolysis.
  12. Cell-type specialization is encoded by specific chromatin topologies.
  13. Identification of ASCL1 as a determinant for human iPSC-derived dopaminergic neurons.
  14. Mediator dynamics during heat shock in budding yeast.
  15. Mapping cis-regulatory elements in the midgestation mouse placenta.
  16. ABHD5 inhibits YAP-induced c-Met overexpression and colon cancer cell stemness via suppressing YAP methylation.
  17. Dynamic expression of SNAI2 in prostate cancer predicts tumor progression and drug sensitivity.
  18. A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease.
  19. ZHX2 promotes HIF1α oncogenic signaling in triple-negative breast cancer.
  20. An ERK5-KLF2 signalling module regulates early embryonic gene expression and telomere rejuvenation in stem cells.
  21. Epromoters function as a hub to recruit key transcription factors required for the inflammatory response.
  22. A large-scale transgenic RNAi screen identifies transcription factors that modulate myofiber size in Drosophila.
  23. A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization.
  24. CircleBase: an integrated resource and analysis platform for human eccDNAs.
  25. Phosphorylation-dependent mitotic SUMOylation drives nuclear envelope-chromatin interactions.
  26. Histone N-terminal acetyltransferase NAA40 links one-carbon metabolism to chemoresistance.
  27. DISCO: a database of Deeply Integrated human Single-Cell Omics data.
  28. Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation.
  29. Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation.
  30. Chromothripsis followed by circular recombination drives oncogene amplification in human cancer.
  31. Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.
  1. Nucleic Acids Res. 2021 Nov 17. pii: gkab1069. [Epub ahead of print]
    Relaxed 3D genome conformation facilitates the pluripotent to totipotent-like state transition in embryonic stem cells.
    Yezhang Zhu, Jiali Yu, Jiahui Gu, Chaoran Xue, Long Zhang, Jiekai Chen, Li Shen.
      The 3D genome organization is crucial for gene regulation. Although recent studies have revealed a uniquely relaxed genome conformation in totipotent early blastomeres of both fertilized and cloned embryos, how weakened higher-order chromatin structure is functionally linked to totipotency acquisition remains elusive. Using low-input Hi-C, ATAC-seq and ChIP-seq, we systematically examined the dynamics of 3D genome and epigenome during pluripotent to totipotent-like state transition in mouse embryonic stem cells (ESCs). The spontaneously converted 2-cell-embryo-like cells (2CLCs) exhibited more relaxed chromatin architecture compared to ESCs, including global weakening of both enhancer-promoter interactions and TAD insulation. While the former correlated with inactivation of ESC enhancers and down-regulation of pluripotent genes, the latter might facilitate contacts between the putative new enhancers arising in 2CLCs and neighboring 2C genes. Importantly, disruption of chromatin organization by depleting CTCF or the cohesin complex promoted the ESC to 2CLC transition. Our results thus establish a critical role of 3D genome organization in totipotency acquisition.
    DOI:  https://doi.org/10.1093/nar/gkab1069
  2. Nat Commun. 2021 Nov 17. 12(1): 6636
    Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors.
    Ryan J Geusz, Allen Wang, Dieter K Lam, Nicholas K Vinckier, Konstantinos-Dionysios Alysandratos, David A Roberts, Jinzhao Wang, Samy Kefalopoulou, Araceli Ramirez, Yunjiang Qiu, Joshua Chiou, Kyle J Gaulton, Bing Ren, Darrell N Kotton, Maike Sander.
      FOXA pioneer transcription factors (TFs) associate with primed enhancers in endodermal organ precursors. Using a human stem cell model of pancreas differentiation, we here discover that only a subset of pancreatic enhancers is FOXA-primed, whereas the majority is unprimed and engages FOXA upon lineage induction. Primed enhancers are enriched for signal-dependent TF motifs and harbor abundant and strong FOXA motifs. Unprimed enhancers harbor fewer, more degenerate FOXA motifs, and FOXA recruitment to unprimed but not primed enhancers requires pancreatic TFs. Strengthening FOXA motifs at an unprimed enhancer near NKX6.1 renders FOXA recruitment pancreatic TF-independent, induces priming, and broadens the NKX6.1 expression domain. We make analogous observations about FOXA binding during hepatic and lung development. Our findings suggest a dual role for FOXA in endodermal organ development: first, FOXA facilitates signal-dependent lineage initiation via enhancer priming, and second, FOXA enforces organ cell type-specific gene expression via indirect recruitment by lineage-specific TFs.
    DOI:  https://doi.org/10.1038/s41467-021-26950-0
  3. Cell. 2021 Nov 08. pii: S0092-8674(21)01279-4. [Epub ahead of print]
    A single-cell atlas of chromatin accessibility in the human genome.
    Kai Zhang, James D Hocker, Michael Miller, Xiaomeng Hou, Joshua Chiou, Olivier B Poirion, Yunjiang Qiu, Yang E Li, Kyle J Gaulton, Allen Wang, Sebastian Preissl, Bing Ren.
      Current catalogs of regulatory sequences in the human genome are still incomplete and lack cell type resolution. To profile the activity of gene regulatory elements in diverse cell types and tissues in the human body, we applied single-cell chromatin accessibility assays to 30 adult human tissue types from multiple donors. We integrated these datasets with previous single-cell chromatin accessibility data from 15 fetal tissue types to reveal the status of open chromatin for ∼1.2 million candidate cis-regulatory elements (cCREs) in 222 distinct cell types comprised of >1.3 million nuclei. We used these chromatin accessibility maps to delineate cell-type-specificity of fetal and adult human cCREs and to systematically interpret the noncoding variants associated with complex human traits and diseases. This rich resource provides a foundation for the analysis of gene regulatory programs in human cell types across tissues, life stages, and organ systems.
    Keywords:  GWAS; chromatin accessibility; cis regulatory elements; enhancers; epigenome; noncoding variants; single cell ATAC-seq
    DOI:  https://doi.org/10.1016/j.cell.2021.10.024
  4. Nucleic Acids Res. 2021 Nov 18. pii: gkab1073. [Epub ahead of print]
    Genome-wide mapping of G-quadruplex structures with CUT&Tag.
    Jing Lyu, Rui Shao, Philip Yuk Kwong Yung, Simon J Elsässer.
      Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect gene expression, DNA methylation, replication fork progression and genome stability. When and how G4 structures form and are resolved remains unclear. Here we report the use of Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping native G4 in mammalian cell lines at high resolution and low background. Mild native conditions used for the procedure retain more G4 structures and provide a higher signal-to-noise ratio than ChIP-based methods. We determine the G4 landscape of mouse embryonic stem cells (ESC), observing widespread G4 formation at active promoters, active and poised enhancers. We discover that the presence of G4 motifs and G4 structures distinguishes active and primed enhancers in mouse ESCs. Upon differentiation to neural progenitor cells (NPC), enhancer G4s are lost. Further, performing R-loop CUT&Tag, we demonstrate the genome-wide co-occurrence of single-stranded DNA, G4s and R loops at promoters and enhancers. We confirm that G4 structures exist independent of ongoing transcription, suggesting an intricate relationship between transcription and non-canonical DNA structures.
    DOI:  https://doi.org/10.1093/nar/gkab1073
  5. J Cell Biol. 2021 Dec 06. pii: e202103078. [Epub ahead of print]220(12):
    High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq).
    Daniel A Bartlett, Vishnu Dileep, Tetsuya Handa, Yasuyuki Ohkawa, Hiroshi Kimura, Steven Henikoff, David M Gilbert.
      Chromatin profiling in single cells has been extremely challenging and almost exclusively limited to histone proteins. In cases where single-cell methods have shown promise, many require highly specialized equipment or cell type-specific protocols and are relatively low throughput. Here, we combine the advantages of tagmentation, linear amplification, and combinatorial indexing to produce a high-throughput single-cell DNA binding site mapping method that is simple, inexpensive, and capable of multiplexing several independent samples per experiment. Targeted insertion of promoters sequencing (TIP-seq) uses Tn5 fused to proteinA to insert a T7 RNA polymerase promoter adjacent to a chromatin protein of interest. Linear amplification of flanking DNA with T7 polymerase before sequencing library preparation provides ∼10-fold higher unique reads per single cell compared with other methods. We applied TIP-seq to map histone modifications, RNA polymerase II (RNAPII), and transcription factor CTCF binding sites in single human and mouse cells.
    DOI:  https://doi.org/10.1083/jcb.202103078
  6. Nat Genet. 2021 Nov 15.
    A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals.
    Daniel Holoch, Michel Wassef, Cecilia Lövkvist, Dina Zielinski, Setareh Aflaki, Bérangère Lombard, Tiphaine Héry, Damarys Loew, Martin Howard, Raphaël Margueron.
      Epigenetic inheritance of gene expression states enables a single genome to maintain distinct cellular identities. How histone modifications contribute to this process remains unclear. Using global chromatin perturbations and local, time-controlled modulation of transcription, we establish the existence of epigenetic memory of transcriptional activation for genes that can be silenced by the Polycomb group. This property emerges during cell differentiation and allows genes to be stably switched after a transient transcriptional stimulus. This transcriptional memory state at Polycomb targets operates in cis; however, rather than relying solely on read-and-write propagation of histone modifications, the memory is also linked to the strength of activating inputs opposing Polycomb proteins, and therefore varies with the cellular context. Our data and computational simulations suggest a model whereby transcriptional memory arises from double-negative feedback between Polycomb-mediated silencing and active transcription. Transcriptional memory at Polycomb targets thus depends not only on histone modifications but also on the gene-regulatory network and underlying identity of a cell.
    DOI:  https://doi.org/10.1038/s41588-021-00964-2
  7. Nucleic Acids Res. 2021 Nov 12. pii: gkab1044. [Epub ahead of print]
    Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones.
    Liudmila V Popova, Prabakaran Nagarajan, Callie M Lovejoy, Benjamin D Sunkel, Miranda L Gardner, Meng Wang, Michael A Freitas, Benjamin Z Stanton, Mark R Parthun.
      A central component of the epigenome is the pattern of histone post-translational modifications that play a critical role in the formation of specific chromatin states. Following DNA replication, nascent chromatin is a 1:1 mixture of parental and newly synthesized histones and the transfer of modification patterns from parental histones to new histones is a fundamental step in epigenetic inheritance. Here we report that loss of HAT1, which acetylates lysines 5 and 12 of newly synthesized histone H4 during replication-coupled chromatin assembly, results in the loss of accessibility of large domains of heterochromatin, termed HAT1-dependent Accessibility Domains (HADs). HADs are mega base-scale domains that comprise ∼10% of the mouse genome. HAT1 globally represses H3 K9 me3 levels and HADs correspond to the regions of the genome that display HAT1-dependent increases in H3 K9me3 peak density. HADs display a high degree of overlap with a subset of Lamin-Associated Domains (LADs). HAT1 is required to maintain nuclear structure and integrity. These results indicate that HAT1 and the acetylation of newly synthesized histones may be critical regulators of the epigenetic inheritance of heterochromatin and suggest a new mechanism for the epigenetic regulation of nuclear lamina-heterochromatin interactions.
    DOI:  https://doi.org/10.1093/nar/gkab1044
  8. Cell Rep. 2021 Nov 16. pii: S2211-1247(21)01473-X. [Epub ahead of print]37(7): 109994
    Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina.
    Pin Lyu, Thanh Hoang, Clayton P Santiago, Eric D Thomas, Andrew E Timms, Haley Appel, Megan Gimmen, Nguyet Le, Lizhi Jiang, Dong Won Kim, Siqi Chen, David F Espinoza, Ariel E Telger, Kurt Weir, Brian S Clark, Timothy J Cherry, Jiang Qian, Seth Blackshaw.
      Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the developing central nervous system. In this study, we use integrated single-cell RNA and single-cell ATAC sequencing (scATAC-seq) analysis in developing mouse and human retina to identify multiple interconnected, evolutionarily conserved GRNs composed of cell-type-specific transcription factors that both activate genes within their own network and inhibit genes in other networks. These GRNs control temporal patterning in primary progenitors, regulate transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirm that NFI transcription factors selectively activate expression of genes promoting late-stage temporal identity in primary retinal progenitors and identify other transcription factors that regulate rod photoreceptor specification in postnatal retina. This study inventories cis- and trans-acting factors that control retinal development and can guide cell-based therapies aimed at replacing retinal neurons lost to disease.
    Keywords:  NFI; development; gene regulatory network; neurogenesis; progenitor; retina; single-cell ATAC-seq; single-cell RNA-seq; temporal patterning; transcription factor
    DOI:  https://doi.org/10.1016/j.celrep.2021.109994
  9. Nucleic Acids Res. 2021 Nov 17. pii: gkab1043. [Epub ahead of print]
    proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.
    Katherine T Decker, Ye Gao, Kevin Rychel, Tahani Al Bulushi, Siddharth M Chauhan, Donghyuk Kim, Byung-Kwan Cho, Bernhard O Palsson.
      The transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motivate its broad dissemination and reuse, which is currently an unmet need in the prokaryotic domain. To fill this gap, we present proChIPdb (prochipdb.org), an information-rich, interactive web database. This website collects public ChIP-seq/-exo data across several prokaryotes and presents them in dashboards that include curated binding sites, nucleotide-resolution genome viewers, and summary plots such as motif enrichment sequence logos. Users can search for TFs of interest or their target genes, download all data, dashboards, and visuals, and follow external links to understand regulons through biological databases and the literature. This initial release of proChIPdb covers diverse organisms, including most major TFs of Escherichia coli, and can be expanded to support regulon discovery across the prokaryotic domain.
    DOI:  https://doi.org/10.1093/nar/gkab1043
  10. Nature. 2021 Nov 18.
    Genome surveillance by HUSH-mediated silencing of intronless mobile elements.
    Marta Seczynska, Stuart Bloor, Sergio Martinez Cuesta, Paul J Lehner.
      All life forms defend their genome against DNA invasion. Eukaryotic cells recognize incoming DNA and limit transcription through repressive chromatin modifications. The human silencing hub (HUSH) complex transcriptionally represses long interspersed element-1 retrotransposons (L1s) and retroviruses through histone H3 Lys9 trimethylation (H3K9me3)1-3. How HUSH recognizes and initiates silencing of these invading genetic elements is unknown. Here we show that HUSH is able to recognize and transcriptionally repress a broad range of long, intronless transgenes. Intron insertion into HUSH-repressed transgenes counteracts repression, even in the absence of intron splicing. HUSH binds transcripts from the target locus, prior to and independent of H3K9me3 deposition, and target transcription is essential for both initiation and propagation of HUSH-mediated H3K9me3. Genomic data reveal how HUSH binds and represses a subset of endogenous intronless genes generated through retrotransposition of cellular mRNAs. Therefore, intronless cDNA, the hallmark of reverse transcription, provides a versatile means to distinguish invading retroelements from host genes and allows HUSH to protect the genome from 'non-self' DNA, despite no prior exposure to the invading element. Our findings reveal the existence of a transcription dependent, genome surveillance system and explain how it provides immediate protection against newly acquired elements while avoiding inappropriate repression of host genes.
    DOI:  https://doi.org/10.1038/s41586-021-04228-1
  11. Oncogene. 2021 Nov 16.
    MMP-9 drives the melanomagenic transcription program through histone H3 tail proteolysis.
    Yonghwan Shin, Sungmin Kim, Nikhil B Ghate, Suhn K Rhie, Woojin An.
      Melanoma is a type of skin cancer that develops in pigment-producing melanocytes and often spreads to other parts of the body. Aberrant gene expression has been considered as a crucial step for increasing the risk of melanomagenesis, but how chromatin reorganization contributes to this pathogenic process is still not well understood. Here we report that matrix metalloproteinase 9 (MMP-9) localizes to the nucleus of melanoma cells and potentiates gene expression by proteolytically clipping the histone H3 N-terminal tail (H3NT). From genome-wide studies, we discovered that growth-regulatory genes are selectively targeted and activated by MMP-9-dependent H3NT proteolysis in melanoma cells. MMP-9 cooperates functionally with p300/CBP because MMP-9 cleaves H3NT in a manner that is dependent on p300/CBP-mediated acetylation of H3K18. The functional significance of MMP-9-dependent H3NT proteolysis is further underscored by the fact that RNAi knockdown and small-molecule inhibition of MMP-9 and p300/CBP impede melanomagenic gene expression and melanoma tumor growth. Together, our data establish new functions and mechanisms for nuclear MMP-9 in promoting melanomagenesis and demonstrate how MMP-9-dependent H3NT proteolysis can be exploited to prevent and treat melanoma skin cancer.
    DOI:  https://doi.org/10.1038/s41388-021-02109-5
  12. Nature. 2021 Nov 17.
    Cell-type specialization is encoded by specific chromatin topologies.
    Warren Winick-Ng, Alexander Kukalev, Izabela Harabula, Luna Zea-Redondo, Dominik Szabó, Mandy Meijer, Leonid Serebreni, Yingnan Zhang, Simona Bianco, Andrea M Chiariello, Ibai Irastorza-Azcarate, Christoph J Thieme, Thomas M Sparks, Sílvia Carvalho, Luca Fiorillo, Francesco Musella, Ehsan Irani, Elena Torlai Triglia, Aleksandra A Kolodziejczyk, Andreas Abentung, Galina Apostolova, Eleanor J Paul, Vedran Franke, Rieke Kempfer, Altuna Akalin, Sarah A Teichmann, Georg Dechant, Mark A Ungless, Mario Nicodemi, Lonnie Welch, Gonçalo Castelo-Branco, Ana Pombo.
      The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1-3. Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi4-6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation7, are invisible with such approaches8. Here we developed immunoGAM, an extension of genome architecture mapping (GAM)2,9, to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation2,10. We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive 'melting' of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.
    DOI:  https://doi.org/10.1038/s41586-021-04081-2
  13. Sci Rep. 2021 Nov 15. 11(1): 22257
    Identification of ASCL1 as a determinant for human iPSC-derived dopaminergic neurons.
    Aaron M Earley, Lena F Burbulla, Dimitri Krainc, Rajeshwar Awatramani.
      During cellular specification, transcription factors orchestrate cellular decisions through gene regulation. By hijacking these transcriptional networks, human pluripotent stem cells (hPSCs) can be specialized into neurons with different molecular identities for the purposes of regenerative medicine and disease modeling. However, molecular fine tuning cell types to match their in vivo counterparts remains a challenge. Directing cell fates often result in blended or incomplete neuron identities. A better understanding of hPSC to neuron gene regulation is needed. Here, we used single cell RNA sequencing to resolve some of these graded molecular identities during human neurogenesis from hPSCs. Differentiation platforms were established to model neural induction from stem cells, and we characterized these differentiated cell types by 10x single cell RNA sequencing. Using single cell trajectory and co-expression analyses, we identified a co-regulated transcription factor module expressing achaete-scute family basic helix-loop-helix transcription factor 1 (ASCL1) and neuronal differentiation 1 (NEUROD1). We then tested the function of these transcription factors in neuron subtype differentiation by gene knockout in a novel human system that reports the expression of tyrosine hydroxylase (TH), the rate limiting enzyme in dopamine synthesis. ASCL1 was identified as a necessary transcription factor for regulating dopaminergic neurotransmitter selection.
    DOI:  https://doi.org/10.1038/s41598-021-01366-4
  14. Genome Res. 2021 Nov 16. pii: gr.275750.121. [Epub ahead of print]
    Mediator dynamics during heat shock in budding yeast.
    Debasish Sarkar, Z Iris Zhu, Elisabeth R Knoll, Emily Paul, David Landsman, Randall H Morse.
      The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates pre-initiation complex (PIC) assembly, only transiently prior to Pol II escape. Interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes this association. However, Mediator occupancy and dynamics have not been examined on a genome-wide scale in yeast grown in nonstandard conditions. Here we investigate Mediator occupancy following heat shock or CdCl2 exposure, with and without depletion of Kin28. We find that Pol II occupancy exhibits similar dependence on Mediator under normal and heat shock conditions. However, while Mediator association increases at many genes upon Kin28 depletion under standard growth conditions, little or no increase is observed at most genes upon heat shock, indicating a more stable association of Mediator after heat shock. Mediator remains associated upstream of the core promoter at genes repressed by heat shock or CdCl2 exposure whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. This persistent association is strongest at promoters that bind the HMGB family member Hmo1, and is reduced but not eliminated in hmo1∆ yeast. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting altered dynamics or stronger engagement with activators under these conditions.
    DOI:  https://doi.org/10.1101/gr.275750.121
  15. Sci Rep. 2021 Nov 16. 11(1): 22331
    Mapping cis-regulatory elements in the midgestation mouse placenta.
    Rebekah R Starks, Haninder Kaur, Geetu Tuteja.
      The placenta is a temporary organ that provides the developing fetus with nutrients, oxygen, and protection in utero. Defects in its development, which may be caused by misregulated gene expression, can lead to devastating outcomes for the mother and fetus. In mouse, placental defects during midgestation commonly lead to embryonic lethality. However, the regulatory mechanisms controlling expression of genes during this period have not been thoroughly investigated. Therefore, we generated and analyzed ChIP-seq data for multiple histone modifications known to mark cis-regulatory regions. We annotated active and poised promoters and enhancers, as well as regions generally associated with repressed gene expression. We found that poised promoters were associated with neuronal development genes, while active promoters were largely associated with housekeeping genes. Active and poised enhancers were associated with placental development genes, though only active enhancers were associated with genes that have placenta-specific expression. Motif analysis within active enhancers identified a large network of transcription factors, including those that have not been previously studied in the placenta and are candidates for future studies. The data generated and genomic regions annotated provide researchers with a foundation for future studies, aimed at understanding how specific genes in the midgestation mouse placenta are regulated.
    DOI:  https://doi.org/10.1038/s41598-021-01664-x
  16. Nat Commun. 2021 Nov 18. 12(1): 6711
    ABHD5 inhibits YAP-induced c-Met overexpression and colon cancer cell stemness via suppressing YAP methylation.
    Yan Gu, Yanrong Chen, Lai Wei, Shuang Wu, Kaicheng Shen, Chengxiang Liu, Yan Dong, Yang Zhao, Yue Zhang, Chi Zhang, Wenling Zheng, Jiangyi He, Yunlong Wang, Yifei Li, Xiaoxin Zhao, Hongwei Wang, Jun Tan, Liting Wang, Qi Zhou, Ganfeng Xie, Houjie Liang, Juanjuan Ou.
      Cancer stemness represents a major source of development and progression of colorectal cancer (CRC). c-Met critically contributes to CRC stemness, but how c-Met is activated in CRC remains elusive. We previously identified the lipolytic factor ABHD5 as an important tumour suppressor gene in CRC. Here, we show that loss of ABHD5 promotes c-Met activation to sustain CRC stemness in a non-canonical manner. Mechanistically, we demonstrate that ABHD5 interacts in the cytoplasm with the core subunit of the SET1A methyltransferase complex, DPY30, thereby inhibiting the nuclear translocation of DPY30 and activity of SET1A. In the absence of ABHD5, DPY30 translocates to the nucleus and supports SET1A-mediated methylation of YAP and histone H3, which sequesters YAP in the nucleus and increases chromatin accessibility to synergistically promote YAP-induced transcription of c-Met, thus promoting the stemness of CRC cells. This study reveals a novel role of ABHD5 in regulating histone/non-histone methylation and CRC stemness.
    DOI:  https://doi.org/10.1038/s41467-021-26967-5
  17. Mol Oncol. 2021 Nov 18.
    Dynamic expression of SNAI2 in prostate cancer predicts tumor progression and drug sensitivity.
    Ying Z Mazzu, YuRou Liao, Subhiksha Nandakumar, Martin Sjöström, Lina E Jehane, Romina Ghale, Barani Govindarajan, Travis A Gerke, Gwo-Shu Mary Lee, Jian-Hua Luo, Sreenivasa R Chinni, Lorelei A Mucci, Felix Y Feng, Philip W Kantoff.
      Prostate cancer is a highly heterogeneous disease, understanding the crosstalk between complex genomic and epigenomic alterations will aid in developing targeted therapeutics. We demonstrate that, even though snail family transcriptional repressor 2 (SNAI2) is frequently amplified in prostate cancer, it is epigenetically silenced in this disease, with dynamic changes in SNAI2 levels showing distinct clinical relevance. Integrative clinical data from 18 prostate cancer cohorts and experimental evidence showed that gene fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2-ERG fusion) is involved in the silencing of SNAI2. We created a silencer score to evaluate epigenetic repression of SNAI2, which can be reversed by treatment with DNA methyltransferase (DNMT) inhibitors and histone deacetylase (HDAC) inhibitors. Silencing of SNAI2 facilitated tumor cell proliferation and luminal differentiation. Furthermore, SNAI2 has a major influence on the tumor microenvironment by reactivating tumor stroma and creating an immunosuppressive microenvironment in prostate cancer. Importantly, SNAI2 expression levels in part determine sensitivity to the cancer drugs dasatinib and panobinostat. For the first time, we defined the distinct clinical relevance of SNAI2 expression at different disease stages. We elucidated how epigenetic silencing of SNAI2 controls the dynamic changes of SNAI2 expression that are essential for tumor initiation and progression, and discovered that restoring SNAI2 expression by treatment with panobinostat enhances dasatinib sensitivity, indicating a new therapeutic strategy for prostate cancer.
    Keywords:  DNA methylation; HDAC inhibitor; SNAI2; TMPRSS2-ERG; dasatinib; panobinostat; prostate cancer
    DOI:  https://doi.org/10.1002/1878-0261.13140
  18. Genome Res. 2021 Nov 15.
    A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease.
    Sumantra Chatterjee, Kameko M Karasaki, Lauren E Fries, Ashish Kapoor, Aravinda Chakravarti.
      The major genetic risk factors for Hirschsprung disease (HSCR) are three common polymorphisms within cis-regulatory elements (CREs) of the receptor tyrosine kinase gene RET, which reduce its expression during enteric nervous system (ENS) development. These risk variants attenuate binding of the transcription factors RARB, GATA2, and SOX10 to their cognate CREs, reduce RET gene expression, and dysregulate other ENS and HSCR genes in the RET-EDNRB gene regulatory network (GRN). Here, we use siRNA, ChIP, and CRISPR-Cas9 deletion analyses in the SK-N-SH cell line to ask how many additional HSCR-associated risk variants reside in RET CREs that affect its gene expression. We identify 22 HSCR-associated variants in candidate RET CREs, of which seven have differential allele-specific in vitro enhancer activity, and four of these seven affect RET gene expression; of these, two enhancers are bound by the transcription factor PAX3. We also show that deleting multiple variant-containing enhancers leads to synergistic effects on RET gene expression. These, coupled with our prior results, show that common sequence variants in at least 10 RET enhancers affect HSCR risk, seven with experimental evidence of affecting RET gene expression, extending the known RET-EDNRB GRN to reveal an extensive regulatory code modulating disease risk at a single gene.
    DOI:  https://doi.org/10.1101/gr.275667.121
  19. Elife. 2021 Nov 15. pii: e70412. [Epub ahead of print]10
    ZHX2 promotes HIF1α oncogenic signaling in triple-negative breast cancer.
    Wentong Fang, Chengheng Liao, Rachel Shi, Jeremy M Simon, Travis S Ptacek, Giada Zurlo, Youqiong Ye, Leng Han, Cheng Fan, Lei Bao, Christopher Llynard Ortiz, Hong-Rui Lin, Ujjawal Manocha, Weibo Luo, Yan Peng, William Y Kim, Lee-Wei Yang, Qing Zhang.
      Triple-negative breast cancer (TNBC) is an aggressive and highly lethal disease, which warrants the critical need to identify new therapeutic targets. We show that Zinc Fingers and Homeoboxes 2 (ZHX2) is amplified or overexpressed in TNBC cell lines and patients. Functionally, depletion of ZHX2 inhibited TNBC cell growth and invasion in vitro, orthotopic tumor growth and spontaneous lung metastasis in vivo. Mechanistically, ZHX2 bound with hypoxia inducible factor (HIF) family members and positively regulated HIF1a activity in TNBC. Integrated ChIP-Seq and gene expression profiling demonstrated that ZHX2 co-occupied with HIF1a on transcriptionally active promoters marked by H3K4me3 and H3K27ac, thereby promoting gene expression. Among the identified ZHX2 and HIF1a co-regulated genes, overexpression of AP2B1, COX20, KDM3A, or PTGES3L could partially rescue TNBC cell growth defect by ZHX2 depletion, suggested that these downstream targets contribute to the oncogenic role of ZHX2 in an accumulative fashion. Furthermore, multiple residues (R491, R581 and R674) on ZHX2 are important in regulating its phenotype, which correspond with their roles on controlling ZHX2 transcriptional activity in TNBC cells. These studies establish that ZHX2 activates oncogenic HIF1a signaling, therefore serving as a potential therapeutic target for TNBC.
    Keywords:  cancer biology; human
    DOI:  https://doi.org/10.7554/eLife.70412
  20. Biochem J. 2021 Nov 15. pii: BCJ20210646. [Epub ahead of print]
    An ERK5-KLF2 signalling module regulates early embryonic gene expression and telomere rejuvenation in stem cells.
    Helen A Brown, Charles Ac Williams, Houjiang Zhou, Diana Rios-Szwed, Rosalia Fernandez-Alonso, Saria Mansoor, Liam McMulkin, Rachel Toth, Robert Gourlay, Julien Peltier, Nora Dieguez-Martinez, Matthias Trost, Jose M Lizcano, Marios P Stavridis, Greg Findlay.
      The ERK5 MAP kinase signalling pathway drives transcription of naïve pluripotency genes in mouse Embryonic Stem Cells (mESCs). However, how ERK5 impacts on other aspects of mESC biology has not been investigated. Here, we employ quantitative proteomic profiling to identify proteins whose expression is regulated by the ERK5 pathway in mESCs. This reveals a function for ERK5 signalling in regulating dynamically expressed early embryonic 2-cell stage (2C) genes including the mESC rejuvenation factor ZSCAN4. ERK5 signalling and ZSCAN4 induction in mESCs increases telomere length, a key rejuvenative process required for prolonged culture. Mechanistically, ERK5 promotes ZSCAN4 and 2C gene expression via transcription of the KLF2 pluripotency transcription factor. Surprisingly, ERK5 also directly phosphorylates KLF2 to drive ubiquitin-dependent degradation, encoding negative-feedback regulation of 2C gene expression. In summary, our data identify a regulatory module whereby ERK5 kinase and transcriptional activities bi-directionally control KLF2 levels to pattern 2C gene transcription and a key mESC rejuvenation process.
    Keywords:  Kruppel-like transcription factors; embryonic stem cells; extracellular signal-regulated kinases; proteomics
    DOI:  https://doi.org/10.1042/BCJ20210646
  21. Nat Commun. 2021 Nov 18. 12(1): 6660
    Epromoters function as a hub to recruit key transcription factors required for the inflammatory response.
    David Santiago-Algarra, Charbel Souaid, Himanshu Singh, Lan T M Dao, Saadat Hussain, Alejandra Medina-Rivera, Lucia Ramirez-Navarro, Jaime A Castro-Mondragon, Nori Sadouni, Guillaume Charbonnier, Salvatore Spicuglia.
      Gene expression is controlled by the involvement of gene-proximal (promoters) and distal (enhancers) regulatory elements. Our previous results demonstrated that a subset of gene promoters, termed Epromoters, work as bona fide enhancers and regulate distal gene expression. Here, we hypothesized that Epromoters play a key role in the coordination of rapid gene induction during the inflammatory response. Using a high-throughput reporter assay we explored the function of Epromoters in response to type I interferon. We find that clusters of IFNa-induced genes are frequently associated with Epromoters and that these regulatory elements preferentially recruit the STAT1/2 and IRF transcription factors and distally regulate the activation of interferon-response genes. Consistently, we identified and validated the involvement of Epromoter-containing clusters in the regulation of LPS-stimulated macrophages. Our findings suggest that Epromoters function as a local hub recruiting the key TFs required for coordinated regulation of gene clusters during the inflammatory response.
    DOI:  https://doi.org/10.1038/s41467-021-26861-0
  22. PLoS Genet. 2021 Nov 15. 17(11): e1009926
    A large-scale transgenic RNAi screen identifies transcription factors that modulate myofiber size in Drosophila.
    Flavia A Graca, Natalie Sheffield, Melissa Puppa, David Finkelstein, Liam C Hunt, Fabio Demontis.
      Myofiber atrophy occurs with aging and in many diseases but the underlying mechanisms are incompletely understood. Here, we have used >1,100 muscle-targeted RNAi interventions to comprehensively assess the function of 447 transcription factors in the developmental growth of body wall skeletal muscles in Drosophila. This screen identifies new regulators of myofiber atrophy and hypertrophy, including the transcription factor Deaf1. Deaf1 RNAi increases myofiber size whereas Deaf1 overexpression induces atrophy. Consistent with its annotation as a Gsk3 phosphorylation substrate, Deaf1 and Gsk3 induce largely overlapping transcriptional changes that are opposed by Deaf1 RNAi. The top category of Deaf1-regulated genes consists of glycolytic enzymes, which are suppressed by Deaf1 and Gsk3 but are upregulated by Deaf1 RNAi. Similar to Deaf1 and Gsk3 overexpression, RNAi for glycolytic enzymes reduces myofiber growth. Altogether, this study defines the repertoire of transcription factors that regulate developmental myofiber growth and the role of Gsk3/Deaf1/glycolysis in this process.
    DOI:  https://doi.org/10.1371/journal.pgen.1009926
  23. Mol Cell. 2021 Nov 12. pii: S1097-2765(21)00909-6. [Epub ahead of print]
    A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization.
    Christos P Zampetidis, Panagiotis Galanos, Andriani Angelopoulou, Yajie Zhu, Aikaterini Polyzou, Timokratis Karamitros, Athanassios Kotsinas, Nefeli Lagopati, Ioanna Mourkioti, Reza Mirzazadeh, Alexandros Polyzos, Silvano Garnerone, Athanasia Mizi, Eduardo G Gusmao, Konstantinos Sofiadis, Zita Gál, Dorthe H Larsen, Dafni-Eleftheria Pefani, Marco Demaria, Aristotelis Tsirigos, Nicola Crosetto, Apolinar Maya-Mendoza, Angelos Papaspyropoulos, Konstantinos Evangelou, Jiri Bartek, Argyris Papantonis, Vassilis G Gorgoulis.
      Oncogene-induced senescence (OIS) is an inherent and important tumor suppressor mechanism. However, if not removed timely via immune surveillance, senescent cells also have detrimental effects. Although this has mostly been attributed to the senescence-associated secretory phenotype (SASP) of these cells, we recently proposed that "escape" from the senescent state is another unfavorable outcome. The mechanism underlying this phenomenon remains elusive. Here, we exploit genomic and functional data from a prototypical human epithelial cell model carrying an inducible CDC6 oncogene to identify an early-acquired recurrent chromosomal inversion that harbors a locus encoding the circadian transcription factor BHLHE40. This inversion alone suffices for BHLHE40 activation upon CDC6 induction and driving cell cycle re-entry of senescent cells, and malignant transformation. Ectopic overexpression of BHLHE40 prevented induction of CDC6-triggered senescence. We provide strong evidence in support of replication stress-induced genomic instability being a causative factor underlying "escape" from oncogene-induced senescence.
    Keywords:  BHLHE40; DNA damage; DNA replication; Hi-C; cancer; chromatin loop; replication stress; senescence
    DOI:  https://doi.org/10.1016/j.molcel.2021.10.017
  24. Nucleic Acids Res. 2021 Nov 18. pii: gkab1104. [Epub ahead of print]
    CircleBase: an integrated resource and analysis platform for human eccDNAs.
    Xiaolu Zhao, Leisheng Shi, Shasha Ruan, Wenjian Bi, Yifan Chen, Lin Chen, Yifan Liu, Mingkun Li, Jie Qiao, Fengbiao Mao.
      Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challenging to interpret the molecular functions of eccDNAs. Here, we present CircleBase (http://circlebase.maolab.org), an integrated resource and analysis platform used to curate and interpret eccDNAs in multiple cell types. CircleBase identifies putative functional eccDNAs by incorporating sequencing datasets, computational predictions, and manual annotations. It classifies them into six sections including targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants. The eccDNA targeting and regulatory networks are displayed by informative visualization tools and then prioritized. Functional enrichment analyses revealed that the top-ranked cancer cell eccDNAs were enriched in oncogenic pathways such as the Ras and PI3K-Akt signaling pathways. In contrast, eccDNAs from healthy individuals were not significantly enriched. CircleBase provides a user-friendly interface for searching, browsing, and analyzing eccDNAs in various cell/tissue types. Thus, it is useful to screen for potential functional eccDNAs and interpret their molecular mechanisms in human cancers and other diseases.
    DOI:  https://doi.org/10.1093/nar/gkab1104
  25. J Cell Biol. 2021 Dec 06. pii: e202103036. [Epub ahead of print]220(12):
    Phosphorylation-dependent mitotic SUMOylation drives nuclear envelope-chromatin interactions.
    Christopher Ptak, Natasha O Saik, Ashwini Premashankar, Diego L Lapetina, John D Aitchison, Ben Montpetit, Richard W Wozniak.
      In eukaryotes, chromatin binding to the inner nuclear membrane (INM) and nuclear pore complexes (NPCs) contributes to spatial organization of the genome and epigenetic programs important for gene expression. In mitosis, chromatin-nuclear envelope (NE) interactions are lost and then formed again as sister chromosomes segregate to postmitotic nuclei. Investigating these processes in S. cerevisiae, we identified temporally and spatially controlled phosphorylation-dependent SUMOylation events that positively regulate postmetaphase chromatin association with the NE. Our work establishes a phosphorylation-mediated targeting mechanism of the SUMO ligase Siz2 to the INM during mitosis, where Siz2 binds to and SUMOylates the VAP protein Scs2. The recruitment of Siz2 through Scs2 is further responsible for a wave of SUMOylation along the INM that supports the assembly and anchorage of subtelomeric chromatin at the INM and localization of an active gene (INO1) to NPCs during the later stages of mitosis and into G1-phase.
    DOI:  https://doi.org/10.1083/jcb.202103036
  26. Oncogene. 2021 Nov 16.
    Histone N-terminal acetyltransferase NAA40 links one-carbon metabolism to chemoresistance.
    Christina Demetriadou, Anastasia Raoukka, Evelina Charidemou, Constantine Mylonas, Christina Michael, Swati Parekh, Costas Koufaris, Paris Skourides, Panagiotis Papageorgis, Peter Tessarz, Antonis Kirmizis.
      Aberrant function of epigenetic modifiers plays an important role not only in the progression of cancer but also the development of drug resistance. N-alpha-acetyltransferase 40 (NAA40) is a highly specific epigenetic enzyme catalyzing the transfer of an acetyl moiety at the N-terminal end of histones H4 and H2A. Recent studies have illustrated the essential oncogenic role of NAA40 in various cancer types but its role in chemoresistance remains unclear. Here, using transcriptomic followed by metabolomic analysis in colorectal cancer (CRC) cells, we demonstrate that NAA40 controls key one-carbon metabolic genes and corresponding metabolites. In particular, through its acetyltransferase activity NAA40 regulates the methionine cycle thereby affecting global histone methylation and CRC cell survival. Importantly, NAA40-mediated metabolic rewiring promotes resistance of CRC cells to antimetabolite chemotherapy in vitro and in xenograft models. Specifically, NAA40 stimulates transcription of the one-carbon metabolic gene thymidylate synthase (TYMS), whose product is targeted by 5-fluorouracil (5-FU) and accordingly in primary CRC tumours NAA40 expression associates with TYMS levels and poorer 5-FU response. Mechanistically, NAA40 activates TYMS by preventing enrichment of repressive H2A/H4S1ph at the nuclear periphery. Overall, these findings define a novel regulatory link between epigenetics and cellular metabolism mediated by NAA40, which is harnessed by cancer cells to evade chemotherapy.
    DOI:  https://doi.org/10.1038/s41388-021-02113-9
  27. Nucleic Acids Res. 2021 Nov 17. pii: gkab1020. [Epub ahead of print]
    DISCO: a database of Deeply Integrated human Single-Cell Omics data.
    Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen.
      The ability to study cellular heterogeneity at single cell resolution is making single-cell sequencing increasingly popular. However, there is no publicly available resource that offers an integrated cell atlas with harmonized metadata that users can integrate new data with. Here, we present DISCO (https://www.immunesinglecell.org/), a database of Deeply Integrated Single-Cell Omics data. The current release of DISCO integrates more than 18 million cells from 4593 samples, covering 107 tissues/cell lines/organoids, 158 diseases, and 20 platforms. We standardized the associated metadata with a controlled vocabulary and ontology system. To allow large scale integration of single-cell data, we developed FastIntegration, a fast and high-capacity version of Seurat Integration. We also developed CELLiD, an atlas guided automatic cell type identification tool. Employing these two tools on the assembled data, we constructed one global atlas and 27 sub-atlases for different tissues, diseases, and cell types. DISCO provides three online tools, namely Online FastIntegration, Online CELLiD, and CellMapper, for users to integrate, annotate, and project uploaded single-cell RNA-seq data onto a selected atlas. Collectively, DISCO is a versatile platform for users to explore published single-cell data and efficiently perform integrated analysis with their own data.
    DOI:  https://doi.org/10.1093/nar/gkab1020
  28. Mol Cell. 2021 Nov 15. pii: S1097-2765(21)00953-9. [Epub ahead of print]
    Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation.
    Olivier Finet, Carlo Yague-Sanz, Lara Katharina Krüger, Phong Tran, Valérie Migeot, Max Louski, Alicia Nevers, Mathieu Rougemaille, Jingjing Sun, Felix G M Ernst, Ludivine Wacheul, Maxime Wery, Antonin Morillon, Peter Dedon, Denis L J Lafontaine, Damien Hermand.
      The epitranscriptome has emerged as a new fundamental layer of control of gene expression. Nevertheless, the determination of the transcriptome-wide occupancy and function of RNA modifications remains challenging. Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent rhodamine labeling. Using Rho-seq, we confirm that the reduction of uridine to dihydrouridine (D) by the Dus reductase enzymes targets tRNAs in E. coli and fission yeast. We find that the D modification is also present on fission yeast mRNAs, particularly those encoding cytoskeleton-related proteins, which is supported by large-scale proteome analyses and ribosome profiling. We show that the α-tubulin encoding mRNA nda2 undergoes Dus3-dependent dihydrouridylation, which affects its translation. The absence of the modification on nda2 mRNA strongly impacts meiotic chromosome segregation, resulting in low gamete viability. Applying Rho-seq to human cells revealed that tubulin mRNA dihydrouridylation is evolutionarily conserved.
    Keywords:  DUS; dihydrouridine; epitranscriptomics; meiosis; yeast
    DOI:  https://doi.org/10.1016/j.molcel.2021.11.003
  29. Commun Biol. 2021 Nov 17. 4(1): 1298
    Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation.
    Sandra Heller, Zhijian Li, Qiong Lin, Ryan Geusz, Markus Breunig, Meike Hohwieler, Xi Zhang, Gopika G Nair, Thomas Seufferlein, Matthias Hebrok, Maike Sander, Cécile Julier, Alexander Kleger, Ivan G Costa.
      Cell type specification during pancreatic development is tightly controlled by a transcriptional and epigenetic network. The precise role of most transcription factors, however, has been only described in mice. To convey such concepts to human pancreatic development, alternative model systems such as pancreatic in vitro differentiation of human pluripotent stem cells can be employed. Here, we analyzed stage-specific RNA-, ChIP-, and ATAC-sequencing data to dissect transcriptional and regulatory mechanisms during pancreatic development. Transcriptome and open chromatin maps of pancreatic differentiation from human pluripotent stem cells provide a stage-specific pattern of known pancreatic transcription factors and indicate ONECUT1 as a crucial fate regulator in pancreas progenitors. Moreover, our data suggest that ONECUT1 is also involved in preparing pancreatic progenitors for later endocrine specification. The dissection of the transcriptional and regulatory circuitry revealed an important role for ONECUT1 within such network and will serve as resource to study human development and disease.
    DOI:  https://doi.org/10.1038/s42003-021-02818-3
  30. Nat Genet. 2021 Nov 15.
    Chromothripsis followed by circular recombination drives oncogene amplification in human cancer.
    Carolina Rosswog, Christoph Bartenhagen, Anne Welte, Yvonne Kahlert, Nadine Hemstedt, Witali Lorenz, Maria Cartolano, Sandra Ackermann, Sven Perner, Wenzel Vogel, Janine Altmüller, Peter Nürnberg, Falk Hertwig, Gudrun Göhring, Esther Lilienweiss, Adrian M Stütz, Jan O Korbel, Roman K Thomas, Martin Peifer, Matthias Fischer.
      The mechanisms behind the evolution of complex genomic amplifications in cancer have remained largely unclear. Using whole-genome sequencing data of the pediatric tumor neuroblastoma, we here identified a type of amplification, termed 'seismic amplification', that is characterized by multiple rearrangements and discontinuous copy number levels. Overall, seismic amplifications occurred in 9.9% (274 of 2,756) of cases across 38 cancer types, and were associated with massively increased copy numbers and elevated oncogene expression. Reconstruction of the development of seismic amplification showed a stepwise evolution, starting with a chromothripsis event, followed by formation of circular extrachromosomal DNA that subsequently underwent repetitive rounds of circular recombination. The resulting amplicons persisted as extrachromosomal DNA circles or had reintegrated into the genome in overt tumors. Together, our data indicate that the sequential occurrence of chromothripsis and circular recombination drives oncogene amplification and overexpression in a substantial fraction of human malignancies.
    DOI:  https://doi.org/10.1038/s41588-021-00951-7
  31. EMBO Rep. 2021 Nov 15. e53054
    Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.
    Mara Mennuni, Roberta Filograna, Andrea Felser, Nina A Bonekamp, Patrick Giavalisco, Oleksandr Lytovchenko, Nils-Göran Larsson.
      Cancer cells depend on mitochondria to sustain their increased metabolic need and mitochondria therefore constitute possible targets for cancer treatment. We recently developed small-molecule inhibitors of mitochondrial transcription (IMTs) that selectively impair mitochondrial gene expression. IMTs have potent antitumor properties in vitro and in vivo, without affecting normal tissues. Because therapy-induced resistance is a major constraint to successful cancer therapy, we investigated mechanisms conferring resistance to IMTs. We employed a CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats)-(CRISP-associated protein 9) whole-genome screen to determine pathways conferring resistance to acute IMT1 treatment. Loss of genes belonging to von Hippel-Lindau (VHL) and mammalian target of rapamycin complex 1 (mTORC1) pathways caused resistance to acute IMT1 treatment and the relevance of these pathways was confirmed by chemical modulation. We also generated cells resistant to chronic IMT treatment to understand responses to persistent mitochondrial gene expression impairment. We report that IMT1-acquired resistance occurs through a compensatory increase of mitochondrial DNA (mtDNA) expression and cellular metabolites. We found that mitochondrial transcription factor A (TFAM) downregulation and inhibition of mitochondrial translation impaired survival of resistant cells. The identified susceptibility and resistance mechanisms to IMTs may be relevant for different types of mitochondria-targeted therapies.
    Keywords:  CRISPR-Cas9 screen; cancer; chemoresistance; inhibitor of mitochondrial transcription; mtDNA
    DOI:  https://doi.org/10.15252/embr.202153054
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