bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2024–11–03
24 papers selected by
Connor Rogerson, University of Cambridge
  1. Transient promoter interactions modulate developmental gene activation.
  2. Large-scale analysis of the integration of enhancer-enhancer signals by promoters.
  3. Optogenetic dissection of transcriptional repression in a multicellular organism.
  4. Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data.
  5. NUP98 fusion proteins and KMT2A-MENIN antagonize PRC1.1 to drive gene expression in AML.
  6. Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells.
  7. m6Am sequesters PCF11 to suppress premature termination and drive neuroblastoma differentiation.
  8. Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.
  9. Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana.
  10. Phosphorylation by JNK switches BRD4 functions.
  11. Common modes of ERK induction resolve into context-specific signalling via emergent networks and cell-type-specific transcriptional repression.
  12. H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos.
  13. Automated live-cell single-molecule tracking in enteroid monolayers reveals transcription factor dynamics probing lineage-determining function.
  14. YY1 is a transcriptional activator of the mouse LINE-1 Tf subfamily.
  15. Progressive plasticity during colorectal cancer metastasis.
  16. A history-dependent integrase recorder of plant gene expression with single-cell resolution.
  17. ASCL1 regulates and cooperates with FOXA2 to drive terminal neuroendocrine phenotype in prostate cancer.
  18. MLL oncoprotein levels influence leukemia lineage identities.
  19. VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers.
  20. PI3K/AKT signaling controls ICM maturation and proper epiblast and primitive endoderm specification in mice.
  21. Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila.
  22. Genome-wide profiling of soybean WRINKLED1 transcription factor binding sites provides insight into seed storage lipid biosynthesis.
  23. ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner.
  24. Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis.
  1. Mol Cell. 2024 Oct 23. pii: S1097-2765(24)00828-1. [Epub ahead of print]
    Transient promoter interactions modulate developmental gene activation.
    Sylvia Mahara, Sonja Prüssing, Valeriia Smialkovska, Samuel Krall, Susannah Holliman, Belinda Blum, Victoria Dachtler, Helena Borgers, Etienne Sollier, Christoph Plass, Angelika Feldmann.
      Transcriptional induction coincides with the formation of various chromatin topologies. Strong evidence supports that gene activation is accompanied by a general increase in promoter-enhancer interactions. However, it remains unclear how these topological changes are coordinated across time and space during transcriptional activation. Here, we combine chromatin conformation capture with transcription and chromatin profiling during an embryonic stem cell (ESC) differentiation time course to determine how 3D genome restructuring is related to transcriptional transitions. This approach allows us to identify distinct topological alterations that are associated with the magnitude of transcriptional induction. We detect transiently formed interactions and demonstrate by genetic deletions that associated distal regulatory elements (DREs), as well as appropriate formation and disruption of these interactions, can contribute to the transcriptional induction of linked genes. Together, our study links topological dynamics to the magnitude of transcriptional induction and detects an uncharacterized type of transcriptionally important DREs.
    Keywords:  Capture-C; chromatin organization; distal regulatory elements; embryonic stem cell differentiation; gene expression; genome topology; histone modifications; temporal dynamics
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.005
  2. Elife. 2024 Oct 28. pii: RP91994. [Epub ahead of print]12
    Large-scale analysis of the integration of enhancer-enhancer signals by promoters.
    Miguel Martinez-Ara, Federico Comoglio, Bas van Steensel.
      Genes are often regulated by multiple enhancers. It is poorly understood how the individual enhancer activities are combined to control promoter activity. Anecdotal evidence has shown that enhancers can combine sub-additively, additively, synergistically, or redundantly. However, it is not clear which of these modes are more frequent in mammalian genomes. Here, we systematically tested how pairs of enhancers activate promoters using a three-way combinatorial reporter assay in mouse embryonic stem cells. By assaying about 69,000 enhancer-enhancer-promoter combinations we found that enhancer pairs generally combine near-additively. This behaviour was conserved across seven developmental promoters tested. Surprisingly, these promoters scale the enhancer signals in a non-linear manner that depends on promoter strength. A housekeeping promoter showed an overall different response to enhancer pairs, and a smaller dynamic range. Thus, our data indicate that enhancers mostly act additively, but promoters transform their collective effect non-linearly.
    Keywords:  chromosomes; compatibility; computational biology; enhancer; gene expression; gene regulation; mouse; promoter; systems biology
    DOI:  https://doi.org/10.7554/eLife.91994
  3. Nat Commun. 2024 Oct 26. 15(1): 9263
    Optogenetic dissection of transcriptional repression in a multicellular organism.
    Jiaxi Zhao, Nicholas C Lammers, Simon Alamos, Yang Joon Kim, Gabriella Martini, Hernan G Garcia.
      Transcriptional control is fundamental to cellular function. However, despite knowing that transcription factors can repress or activate specific genes, how these functions are implemented at the molecular level has remained elusive, particularly in the endogenous context of developing animals. Here, we combine optogenetics, single-cell live-imaging, and mathematical modeling to study how a zinc-finger repressor, Knirps, induces switch-like transitions into long-lived quiescent states. Using optogenetics, we demonstrate that repression is rapidly reversible (~1 min) and memoryless. Furthermore, we show that the repressor acts by decreasing the frequency of transcriptional bursts in a manner consistent with an equilibrium binding model. Our results provide a quantitative framework for dissecting the in vivo biochemistry of eukaryotic transcriptional regulation.
    DOI:  https://doi.org/10.1038/s41467-024-53539-0
  4. Genome Biol. 2024 Oct 31. 25(1): 284
    Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data.
    Xiaoting Li, Lucas A N Melo, Harmen J Bussemaker.
       BACKGROUND: Transcription factors (TFs) bind to DNA in a highly sequence-specific manner. This specificity manifests itself in vivo as differences in TF occupancy between the two alleles at heterozygous loci. Genome-scale assays such as ChIP-seq currently are limited in their power to detect allele-specific binding (ASB) both in terms of read coverage and representation of individual variants in the cell lines used. This makes prediction of allelic differences in TF binding from sequence alone desirable, provided that the reliability of such predictions can be quantitatively assessed.
    RESULTS: We here propose methods for benchmarking sequence-to-affinity models for TF binding in terms of their ability to predict allelic imbalances in ChIP-seq counts. We use a likelihood function based on an over-dispersed binomial distribution to aggregate evidence for allelic preference across the genome without requiring statistical significance for individual variants. This allows us to systematically compare predictive performance when multiple binding models for the same TF are available. To facilitate the de novo inference of high-quality models from paired-end in vivo binding data such as ChIP-seq, ChIP-exo, and CUT&Tag without read mapping or peak calling, we introduce an extensible reimplementation of our biophysically interpretable machine learning framework named PyProBound. Explicitly accounting for assay-specific bias in DNA fragmentation rate when training on ChIP-seq yields improved TF binding models. Moreover, we show how PyProBound can leverage our threshold-free ASB likelihood function to perform de novo motif discovery using allele-specific ChIP-seq counts.
    CONCLUSION: Our work provides new strategies for predicting the functional impact of non-coding variants.
    Keywords:  Allele-specific binding; Biophysically interpretable machine learning; CTCF, EBF1, PU.1/SPI1; ChIP-seq, ChIP-exo, CUT&Tag; Gene expression regulation; Motif discovery; Non-coding variants; Statistical modeling; Transcription factors
    DOI:  https://doi.org/10.1186/s13059-024-03424-2
  5. Cell Rep. 2024 Oct 29. pii: S2211-1247(24)01252-X. [Epub ahead of print]43(11): 114901
    NUP98 fusion proteins and KMT2A-MENIN antagonize PRC1.1 to drive gene expression in AML.
    Emily B Heikamp, Cynthia Martucci, Jill A Henrich, Dana S Neel, Sanisha Mahendra-Rajah, Hannah Rice, Daniela V Wenge, Florian Perner, Yanhe Wen, Charlie Hatton, Scott A Armstrong.
      Control of stem cell-associated genes by Trithorax group (TrxG) and Polycomb group (PcG) proteins is frequently misregulated in cancer. In leukemia, oncogenic fusion proteins hijack the TrxG homolog KMT2A and disrupt PcG activity to maintain pro-leukemogenic gene expression, though the mechanisms by which oncofusion proteins antagonize PcG proteins remain unclear. Here, we define the relationship between NUP98 oncofusion proteins and the non-canonical polycomb repressive complex 1.1 (PRC1.1) in leukemia using Menin-KMT2A inhibitors and targeted degradation of NUP98 fusion proteins. Eviction of the NUP98 fusion-Menin-KMT2A complex from chromatin is not sufficient to silence pro-leukemogenic genes. In the absence of PRC1.1, key oncogenes remain transcriptionally active. Transition to a repressed chromatin state requires the accumulation of PRC1.1 and repressive histone modifications. We show that PRC1.1 loss leads to resistance to small-molecule Menin-KMT2A inhibitors in vivo. Therefore, a critical function of oncofusion proteins that hijack Menin-KMT2A activity is antagonizing repressive chromatin complexes.
    Keywords:  CP: Cancer; CP: Molecular biology; acute myeloid leukemia; chromatin complex; lysine methyltransferase 2A; menin; nascent transcriptomics; non-canonical polycomb repressive complex 1.1; nucleoporin 98-rearrangement; oncogenic fusion protein
    DOI:  https://doi.org/10.1016/j.celrep.2024.114901
  6. Nat Cell Biol. 2024 Oct 31.
    Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells.
    Jingchao Zhang, Greg Donahue, Michael B Gilbert, Tomer Lapidot, Dario Nicetto, Kenneth S Zaret.
      H3K9me3 heterochromatin, established by lysine methyltransferases (KMTs) and compacted by heterochromatin protein 1 (HP1) isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3 heterochromatin stability is presently limited to individual domains and DNA repeats. Here we engineered Suv39h2-knockout mouse embryonic stem cells to degrade remaining two H3K9me3 KMTs within 1 hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12-24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A 'binary switch' governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMT depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening and exit from pluripotency within 12 h. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3 heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.
    DOI:  https://doi.org/10.1038/s41556-024-01547-z
  7. Mol Cell. 2024 Oct 23. pii: S1097-2765(24)00827-X. [Epub ahead of print]
    m6Am sequesters PCF11 to suppress premature termination and drive neuroblastoma differentiation.
    Huihui An, Yifan Hong, Yeek Teck Goh, Casslynn W Q Koh, Shahzina Kanwal, Yi Zhang, Zhaoqi Lu, Phoebe M L Yap, Suat Peng Neo, Chun-Ming Wong, Alice S T Wong, Yang Yu, Jessica Sook Yuin Ho, Jayantha Gunaratne, Wee Siong Sho Goh.
      N6,2'-O-dimethyladenosine (m6Am) is an abundant mRNA modification that impacts multiple diseases, but its function remains controversial because the m6Am reader is unknown. Using quantitative proteomics, we identified transcriptional terminator premature cleavage factor II (PCF11) as a m6Am-specific reader in human cells. Direct quantification of mature versus nascent RNAs reveals that m6Am does not regulate mRNA stability but promotes nascent transcription. Mechanistically, m6Am functions by sequestering PCF11 away from proximal RNA polymerase II (RNA Pol II). This suppresses PCF11 from dissociating RNA Pol II near transcription start sites, thereby promoting full-length transcription of m6Am-modified RNAs. m6Am's unique relationship with PCF11 means m6Am function is enhanced when PCF11 is reduced, which occurs during all-trans-retinoic-acid (ATRA)-induced neuroblastoma-differentiation therapy. Here, m6Am promotes expression of ATF3, which represses neuroblastoma biomarker MYCN. Depleting m6Am suppresses MYCN repression in ATRA-treated neuroblastoma and maintains their tumor-stem-like properties. Collectively, we characterize m6Am as an anti-terminator RNA modification that suppresses premature termination and modulates neuroblastoma's therapeutic response.
    Keywords:  PCF11; m(6)Am; neuroblastoma; premature transcription termination
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.004
  8. Dev Cell. 2024 Oct 29. pii: S1534-5807(24)00603-8. [Epub ahead of print]
    Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.
    Rinaldo Catta-Preta, Susan Lindtner, Athena Ypsilanti, Nicolas Seban, James D Price, Armen Abnousi, Linda Su-Feher, Yurong Wang, Karol Cichewicz, Sally A Boerma, Ivan Juric, Ian R Jones, Jennifer A Akiyama, Ming Hu, Yin Shen, Axel Visel, Len A Pennacchio, Diane E Dickel, John L R Rubenstein, Alex S Nord.
      Transcription factors (TFs) bind combinatorially to cis-regulatory elements, orchestrating transcriptional programs. Although studies of chromatin state and chromosomal interactions have demonstrated dynamic neurodevelopmental cis-regulatory landscapes, parallel understanding of TF interactions lags. To elucidate combinatorial TF binding driving mouse basal ganglia development, we integrated chromatin immunoprecipitation sequencing (ChIP-seq) for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and gene expression data, and functional enhancer assays. We identified sets of putative regulatory elements with shared TF binding (TF-pRE modules) that orchestrate distinct processes of GABAergic neurogenesis and suppress other cell fates. The majority of pREs were bound by one or two TFs; however, a small proportion were extensively bound. These sequences had exceptional evolutionary conservation and motif density, complex chromosomal interactions, and activity as in vivo enhancers. Our results provide insights into the combinatorial TF-pRE interactions that activate and repress expression programs during telencephalon neurogenesis and demonstrate the value of TF binding toward modeling developmental transcriptional wiring.
    Keywords:  GABAergic cortical interneurons; chromatin conformation; combinatorial TF binding; evolutionary conservation; gene regulatory network; neurogenesis; transcription factors
    DOI:  https://doi.org/10.1016/j.devcel.2024.10.004
  9. Nat Commun. 2024 Oct 29. 15(1): 9308
    Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana.
    Anna-Maria Göbel, Sida Zhou, Zhidan Wang, Sofia Tzourtzou, Axel Himmelbach, Shiwei Zheng, Mónica Pradillo, Chang Liu, Hua Jiang.
      In eukaryotes, topologically associating domains (TADs) organize the genome into functional compartments. While TAD-like structures are common in mammals and many plants, they are challenging to detect in Arabidopsis thaliana. Here, we demonstrate that Arabidopsis PDS5 proteins play a negative role in TAD-like domain formation. Through Hi-C analysis, we show that mutations in PDS5 genes lead to the widespread emergence of enhanced TAD-like domains throughout the Arabidopsis genome, excluding pericentromeric regions. These domains exhibit increased chromatin insulation and enhanced chromatin interactions, without significant changes in gene expression or histone modifications. Our results suggest that PDS5 proteins are key regulators of genome architecture, influencing 3D chromatin organization independently of transcriptional activity. This study provides insights into the unique chromatin structure of Arabidopsis and the broader mechanisms governing plant genome folding.
    DOI:  https://doi.org/10.1038/s41467-024-53760-x
  10. Mol Cell. 2024 Oct 17. pii: S1097-2765(24)00821-9. [Epub ahead of print]
    Phosphorylation by JNK switches BRD4 functions.
    Ballachanda N Devaiah, Amit Kumar Singh, Jie Mu, Qingrong Chen, Daoud Meerzaman, Dinah S Singer.
      Bromodomain 4 (BRD4), a key regulator with pleiotropic functions, plays crucial roles in cancers and cellular stress responses. It exhibits dual functionality: chromatin-bound BRD4 regulates remodeling through its histone acetyltransferase (HAT) activity, while promoter-associated BRD4 regulates transcription through its kinase activity. Notably, chromatin-bound BRD4 lacks kinase activity, and RNA polymerase II (RNA Pol II)-bound BRD4 exhibits no HAT activity. This study unveils one mechanism underlying BRD4's functional switch. In response to diverse stimuli, c-Jun N-terminal kinase (JNK)-mediated phosphorylation of human BRD4 at Thr1186 and Thr1212 triggers its transient release from chromatin, disrupting its HAT activity and potentiating its kinase activity. Released BRD4 directly interacts with and phosphorylates RNA Pol II, PTEFb, and c-Myc, thereby promoting transcription of target genes involved in immune and inflammatory responses. JNK-mediated BRD4 functional switching induces CD8 expression in thymocytes and epithelial-to-mesenchymal transition (EMT) in prostate cancer cells. These findings elucidate the mechanism by which BRD4 transitions from a chromatin regulator to a transcriptional activator.
    Keywords:  BRD4; EMT; JNK; cellular stress; chromatin decompaction; histone acetyltransferase; kinase; phospho-BRD4; thymocyte stimulation; transcription activation
    DOI:  https://doi.org/10.1016/j.molcel.2024.09.030
  11. Development. 2024 Nov 01. pii: dev202842. [Epub ahead of print]151(21):
    Common modes of ERK induction resolve into context-specific signalling via emergent networks and cell-type-specific transcriptional repression.
    Marta Perera, Joshua M Brickman.
      Fibroblast Growth Factor signalling via ERK exerts diverse roles in development and disease. In mammalian preimplantation embryos and naïve pluripotent stem cells ERK promotes differentiation, whereas in primed pluripotent states closer to somatic differentiation ERK sustains self-renewal. How can the same pathway produce different outcomes in two related cell types? To explore context-dependent ERK signalling we generated cell and mouse lines that allow for tissue- and time-specific ERK activation. Using these tools, we find that specificity in ERK response is mostly mediated by repression of transcriptional targets that occur in tandem with reductions in chromatin accessibility at regulatory regions. Furthermore, immediate early ERK responses are largely shared by different cell types but produce cell-specific programmes as these responses interface with emergent networks in the responding cells. Induction in naïve pluripotency is accompanied by chromatin changes, whereas in later stages it is not, suggesting that chromatin context does not shape signalling response. Altogether, our data suggest that cell-type-specific responses to ERK signalling exploit the same immediate early response, but then sculpt it to specific lineages via repression of distinct cellular programmes.
    Keywords:  Chromatin; ERK; FGF; Pluripotency; Signalling; Transcription
    DOI:  https://doi.org/10.1242/dev.202842
  12. Nat Cell Biol. 2024 Oct 31.
    H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos.
    Masahiro Matsuwaka, Mami Kumon, Azusa Inoue.
      Facultative heterochromatin is formed by Polycomb repressive complex 2 (PRC2)-deposited H3K27 trimethylation (H3K27me3) and PRC1-deposited H2AK119 mono-ubiquitylation (H2AK119ub1). How it is newly established after fertilization remains unclear. To delineate the establishment kinetics, here we profiled the temporal dynamics of H3K27 dimethylation (H3K27me2), which represents the de novo PRC2 catalysis, in mouse preimplantation embryos. H3K27me2 is newly deposited at CpG islands (CGIs), the paternal X chromosome (Xp) and putative enhancers during the eight-cell-to-morula transition, all of which follow H2AK119ub1 deposition. We found that JARID2, a PRC2.2-specific accessory protein possessing an H2AK119ub1-binding ability, colocalizes with SUZ12 at CGIs and Xp in morula embryos. Upon JARID2 depletion, SUZ12 chromatin binding and H3K27me2 deposition were attenuated and H3K27 acetylation at putative enhancers was increased in morulae and subsequently H3K27me3 failed to be deposited in blastocysts. These data reveal that facultative heterochromatin is established by PRC2.2-driven stepwise H3K27 methylation along pre-deposited H2AK119ub1 during early embryogenesis.
    DOI:  https://doi.org/10.1038/s41556-024-01553-1
  13. Cell Rep. 2024 Oct 29. pii: S2211-1247(24)01265-8. [Epub ahead of print]43(11): 114914
    Automated live-cell single-molecule tracking in enteroid monolayers reveals transcription factor dynamics probing lineage-determining function.
    Nike Walther, Sathvik Anantakrishnan, Thomas G W Graham, Gina M Dailey, Robert Tjian, Xavier Darzacq.
      Lineage transcription factors (TFs) provide one regulatory level of differentiation crucial for the generation and maintenance of healthy tissues. To probe TF function by measuring their dynamics during adult intestinal homeostasis, we established HILO-illumination-based live-cell single-molecule tracking (SMT) in mouse small intestinal enteroid monolayers recapitulating tissue differentiation hierarchies in vitro. To increase the throughput, capture cellular features, and correlate morphological characteristics with diffusion parameters, we developed an automated imaging and analysis pipeline, broadly applicable to two-dimensional culture systems. Studying two absorptive lineage-determining TFs, we found an expression level-independent contrasting diffusive behavior: while Hes1, key determinant of absorptive lineage commitment, displays a large cell-to-cell variability and an average fraction of DNA-bound molecules of ∼32%, Hnf4g, conferring enterocyte identity, exhibits more uniform dynamics and a bound fraction of ∼56%. Our results suggest that TF diffusive behavior could indicate the progression of differentiation and modulate early versus late differentiation within a lineage.
    Keywords:  2D enteroid monolayer culture; CP: Developmental biology; CP: Genomics; automated imaging; cellular feature extraction; cellular protein diffusion; cellular protein self-association; cluster analysis based on protein diffusion behavior; differentiation; intestinal absorptive lineage; live-cell single-molecule tracking; mouse small intestinal organoid; protein diffusion correlation; transcription factor
    DOI:  https://doi.org/10.1016/j.celrep.2024.114914
  14. Nucleic Acids Res. 2024 Oct 26. pii: gkae949. [Epub ahead of print]
    YY1 is a transcriptional activator of the mouse LINE-1 Tf subfamily.
    Karabi Saha, Grace I Nielsen, Raj Nandani, Yizi Zhang, Lingqi Kong, Ping Ye, Wenfeng An.
      Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable element in human and mouse genomes. L1 transcription is controlled by an internal RNA polymerase II promoter in the 5' untranslated region (5'UTR) of a full-length L1. It has been shown that transcription factor YY1 binds to a conserved sequence at the 5' end of the human L1 5'UTR and primarily dictates where transcription initiates. Putative YY1-binding motifs have been predicted in the 5'UTRs of two distinct mouse L1 subfamilies, Tf and Gf. Using site-directed mutagenesis, in vitro binding and gene knockdown assays, we experimentally tested the role of YY1 in mouse L1 transcription. Our results indicate that Tf, but not Gf subfamily, harbors functional YY1-binding sites in 5'UTR monomers and YY1 functions as a transcriptional activator for the mouse Tf subfamily. Activation of Tf transcription by YY1 during early embryogenesis is also supported by a reanalysis of published zygotic knockdown data. Furthermore, YY1-binding motifs are solely responsible for the synergistic interaction between Tf monomers, consistent with a model wherein distant monomers act as enhancers for mouse L1 transcription. The abundance of YY1-binding sites in Tf elements also raise important implications for gene regulation across the genome.
    DOI:  https://doi.org/10.1093/nar/gkae949
  15. Nature. 2024 Oct 30.
    Progressive plasticity during colorectal cancer metastasis.
    A R Moorman, E K Benitez, F Cambuli, Q Jiang, A Mahmoud, M Lumish, S Hartner, S Balkaran, J Bermeo, S Asawa, C Firat, A Saxena, F Wu, A Luthra, C Burdziak, Y Xie, V Sgambati, K Luckett, Y Li, Z Yi, I Masilionis, K Soares, E Pappou, R Yaeger, P Kingham, W Jarnagin, P Paty, M R Weiser, L Mazutis, M D'Angelica, J Shia, J Garcia-Aguilar, T Nawy, T J Hollmann, R Chaligné, F Sanchez-Vega, R Sharma, D Pe'er, K Ganesh.
      As cancers progress, they become increasingly aggressive-metastatic tumours are less responsive to first-line therapies than primary tumours, they acquire resistance to successive therapies and eventually cause death1,2. Mutations are largely conserved between primary and metastatic tumours from the same patients, suggesting that non-genetic phenotypic plasticity has a major role in cancer progression and therapy resistance3-5. However, we lack an understanding of metastatic cell states and the mechanisms by which they transition. Here, in a cohort of biospecimen trios from same-patient normal colon, primary and metastatic colorectal cancer, we show that, although primary tumours largely adopt LGR5+ intestinal stem-like states, metastases display progressive plasticity. Cancer cells lose intestinal cell identities and reprogram into a highly conserved fetal progenitor state before undergoing non-canonical differentiation into divergent squamous and neuroendocrine-like states, a process that is exacerbated in metastasis and by chemotherapy and is associated with poor patient survival. Using matched patient-derived organoids, we demonstrate that metastatic cells exhibit greater cell-autonomous multilineage differentiation potential in response to microenvironment cues compared with their intestinal lineage-restricted primary tumour counterparts. We identify PROX1 as a repressor of non-intestinal lineage in the fetal progenitor state, and show that downregulation of PROX1 licenses non-canonical reprogramming.
    DOI:  https://doi.org/10.1038/s41586-024-08150-0
  16. Nat Commun. 2024 Oct 30. 15(1): 9362
    A history-dependent integrase recorder of plant gene expression with single-cell resolution.
    Cassandra J Maranas, Wesley George, Sarah K Scallon, Sydney VanGilder, Jennifer L Nemhauser, Sarah Guiziou.
      During development, most cells experience a progressive restriction of fate that ultimately results in a fully differentiated mature state. Understanding more about the gene expression patterns that underlie developmental programs can inform engineering efforts for new or optimized forms. Here, we present a four-state integrase-based recorder of gene expression history and demonstrate its use in tracking gene expression events in Arabidopsis thaliana in two developmental contexts: lateral root initiation and stomatal differentiation. The recorder uses two serine integrases to mediate sequential DNA recombination events, resulting in step-wise, history-dependent switching between expression of fluorescent reporters. By using promoters that express at different times along each of the two differentiation pathways to drive integrase expression, we tie fluorescent status to an ordered progression of gene expression along the developmental trajectory. In one snapshot of a mature tissue, our recorder is able to reveal past gene expression with single cell resolution. In this way, we are able to capture heterogeneity in stomatal development, confirming the existence of two alternate paths of differentiation.
    DOI:  https://doi.org/10.1038/s41467-024-53716-1
  17. JCI Insight. 2024 Oct 29. pii: e185952. [Epub ahead of print]
    ASCL1 regulates and cooperates with FOXA2 to drive terminal neuroendocrine phenotype in prostate cancer.
    Shaghayegh Nouruzi, Takeshi Namekawa, Nakisa Tabrizian, Maxim Kobelev, Olena Sivak, Joshua M Scurll, Cassandra Jingjing Cui, Dwaipayan Ganguli, Amina Zoubeidi.
      Lineage plasticity mediates resistance to androgen receptor pathway inhibitors (ARPIs) and progression from adenocarcinoma to neuroendocrine prostate cancer (NEPC), a highly aggressive and poorly understood subtype. ASCL1 has emerged as a central regulator of the lineage plasticity driving neuroendocrine differentiation. Here, we showed that ASCL1 was reprogrammed in ARPI-induced transition to the terminal NEPC and identified that the ASCL1 binding pattern tailored the expression of lineage-determinant transcription factor combinations that underlying discrete terminal NEPC identity. Notably, we identified FOXA2 as a major co-factor of ASCL1 in terminal NEPC, which is highly expressed in ASCL1-driven NEPC. Mechanistically, FOXA2 and ASCL1 interacted and worked in concert to orchestrate terminal neuronal differentiation. We identified that Prospero-Related Homeobox 1 was a target of ASCL1 and FOXA2. Targeting prospero-related homeobox 1 abrogated neuroendocrine characteristics and led to a decrease in cell proliferation in vitro and tumor growth in vivo. Our findings provide insights into the molecular conduit underlying the interplay between different lineage-determinant transcription factors to support the neuroendocrine identity and nominate prospero-related homeobox 1 as a potential target in ASCL1 high NEPC.
    Keywords:  Cell biology; Epigenetics; Neuroendocrine regulation; Prostate cancer
    DOI:  https://doi.org/10.1172/jci.insight.185952
  18. Nat Commun. 2024 Oct 29. 15(1): 9341
    MLL oncoprotein levels influence leukemia lineage identities.
    Derek H Janssens, Melodie Duran, Dominik J Otto, Weifang Wu, Yiling Xu, Danielle Kirkey, Charles G Mullighan, Joanna S Yi, Soheil Meshinchi, Jay F Sarthy, Kami Ahmad, Steven Henikoff.
      Chromosomal translocations involving the mixed-lineage leukemia (MLL) locus generate potent oncogenic fusion proteins (oncoproteins) that disrupt regulation of developmental gene expression. By profiling the oncoprotein-target sites of 36 broadly representative MLL-rearranged leukemia samples, including three samples that underwent a lymphoid-to-myeloid lineage-switching event in response to therapy, we find the genomic enrichment of the oncoprotein is highly variable between samples and subject to dynamic regulation. At high levels of expression, the oncoproteins preferentially activate either an acute lymphoblastic leukemia (ALL) program, enriched for pro-B-cell genes, or an acute myeloid leukemia (AML) program, enriched for hematopoietic-stem-cell genes. The fusion-partner-specific-binding patterns over these gene sets are highly correlated with the prevalence of each mutation in ALL versus AML. In lineage-switching samples the oncoprotein levels are reduced and the oncoproteins preferentially activate granulocyte-monocyte progenitor (GMP) genes. In a sample that lineage switched during treatment with the menin inhibitor revumenib, the oncoprotein and menin are reduced to undetectable levels, but ENL, a transcriptional cofactor of the oncoprotein, persists on numerous oncoprotein-target loci, including genes in the GMP-like lineage-switching program. We propose MLL oncoproteins promote lineage-switching events through dynamic chromatin binding at lineage-specific target genes, and may support resistance to menin inhibitors through similar changes in chromatin occupancy.
    DOI:  https://doi.org/10.1038/s41467-024-53399-8
  19. Nucleic Acids Res. 2024 Oct 29. pii: gkae940. [Epub ahead of print]
    VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers.
    Michael Kosicki, Fotis A Baltoumas, Guy Kelman, Joshua Boverhof, Yeongshnn Ong, Laura E Cook, Diane E Dickel, Georgios A Pavlopoulos, Len A Pennacchio, Axel Visel.
      Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.
    DOI:  https://doi.org/10.1093/nar/gkae940
  20. Dev Cell. 2024 Oct 22. pii: S1534-5807(24)00601-4. [Epub ahead of print]
    PI3K/AKT signaling controls ICM maturation and proper epiblast and primitive endoderm specification in mice.
    Anna Geiselmann, Adèle Micouin, Sandrine Vandormael-Pournin, Vincent Laville, Almira Chervova, Sébastien Mella, Pablo Navarro, Michel Cohen-Tannoudji.
      The inner cell mass (ICM) of early mouse embryos is specified into epiblast (Epi) and primitive endoderm (PrE) lineages during blastocyst formation. The antagonistic transcription factors (TFs) NANOG and GATA-binding protein 6 (GATA6) in combination with fibroblast growth factor (FGF)/extracellular-signal-regulated kinase (ERK) signaling are central actors in ICM fate choice. However, what initiates the specification of ICM progenitors into Epi or PrE and whether other factors are involved in this process has not been fully understood yet. Here, we show that phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) is constitutively active during preimplantation development. Using pharmacological inhibition, we demonstrate that PI3K/AKT enables the formation of a functional ICM capable of giving rise to both the Epi and the PrE: it maintains the expression of the TF NANOG, which specifies the Epi, and confers responsiveness to FGF4, which is essential for PrE specification. Our work thus identifies PI3K/AKT signaling as an upstream regulator controlling the molecular events required for both Epi and PrE specification.
    Keywords:  FGF4; FOXO3; GSK3; NANOG; epiblast; inner cell mass; lineage specification; mTOR; mouse preimplantation embryo; primitive endoderm
    DOI:  https://doi.org/10.1016/j.devcel.2024.10.001
  21. Nucleic Acids Res. 2024 Oct 29. pii: gkae933. [Epub ahead of print]
    Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila.
    Xianhong Zhang, Shao-Bo Liang, Zhuoyun Yi, Zhaohui Qiao, Bo Xu, Huichao Geng, Honghong Wang, Xinhua Yin, Mingliang Tang, Wanzhong Ge, Yong-Zhen Xu, Kaiwei Liang, Yu-Jie Fan, Liang Chen.
      R-loops are involved in many biological processes in cells, yet the regulatory principles for R-loops in vivo and their impact on development remain to be explored. Here, we modified the CUT&Tag strategy to profile R-loops in Drosophila at multiple developmental stages. While high GC content promotes R-loop formation in mammalian cells, it is not required in Drosophila. In contrast, RNAPII abundance appears to be a universal inducing factor for R-loop formation, including active promoters and enhancers, and H3K27me3 decorated repressive regions and intergenic repeat sequences. Importantly, such a regulatory relationship is dynamically maintained throughout development, and development-related transcription factors may regulate RNAPII activation and R-loop dynamics. By ablating Spt6, we further showed the global R-loop induction coupled with RNAPII pausing. Importantly, depending on the gene length, genes underwent up- or down-regulation, both of which were largely reversed by rnh1 overexpression, suggesting that R-loops play a significant role in the divergent regulation of transcription by Spt6 ablation. DNA damage, defects in survival, and cuticle development were similarly alleviated by rnh1 overexpression. Altogether, our findings indicate that dynamic R-loop regulation is dictated by RNAPII pausing and transcription activity, and plays a feedback role in gene regulation, genome stability maintenance, and Drosophila development.
    DOI:  https://doi.org/10.1093/nar/gkae933
  22. Proc Natl Acad Sci U S A. 2024 Nov 05. 121(45): e2415224121
    Genome-wide profiling of soybean WRINKLED1 transcription factor binding sites provides insight into seed storage lipid biosynthesis.
    Leonardo Jo, Julie M Pelletier, Robert B Goldberg, John J Harada.
      Understanding the regulatory mechanisms controlling storage lipid accumulation will inform strategies to enhance seed oil quality and quantity in crop plants. The WRINKLED1 transcription factor (WRI1 TF) is a central regulator of lipid biosynthesis. We characterized the genome-wide binding profile of soybean (Gm)WRI1 and show that the TF directly regulates genes encoding numerous enzymes and proteins in the fatty acid and triacylglycerol biosynthetic pathways. GmWRI1 binds primarily to regions downstream of target gene transcription start sites. We showed that GmWRI1-bound regions are enriched for the canonical WRI1 DNA binding element, the ACTIVATOR of Spomin::LUC1/WRI1 (AW) Box (CNTNGNNNNNNNCG), and another DNA motif, the CNC Box (CNCCNCC). Functional assays showed that both DNA elements mediate transcriptional activation by GmWRI1. We also show that GmWRI1 works in concert with other TFs to establish a regulatory state that promotes fatty acid and triacylglycerol biosynthesis. In particular, comparison of genes targeted directly by GmWRI1 and by GmLEC1, a central regulator of the maturation phase of seed development, reveals that the two TFs act in a positive feedback subcircuit to control fatty acid and triacylglycerol biosynthesis. Together, our results provide unique insights into the genetic circuitry in which GmWRI1 participates to regulate storage lipid accumulation during seed development.
    Keywords:  embryo; fatty acids; triacylglycerol
    DOI:  https://doi.org/10.1073/pnas.2415224121
  23. Nucleic Acids Res. 2024 Oct 26. pii: gkae926. [Epub ahead of print]
    ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner.
    Tim Marius Wunderlich, Chandrika Deshpande, Lena W Paasche, Tobias Friedrich, Felix Diegmüller, Elias Haddad, Carlotta Kreienbaum, Haniya Naseer, Sophie E Stebel, Nadine Daus, Jörg Leers, Jie Lan, Van Tuan Trinh, Olalla Vázquez, Falk Butter, Marek Bartkuhn, Joel P Mackay, Sandra B Hake.
      The evolutionarily conserved histone variant H2A.Z plays a crucial role in various DNA-based processes, but the mechanisms underlying its activity are not completely understood. Recently, we identified the zinc finger (ZF) protein ZNF512B as a protein associated with H2A.Z, HMG20A and PWWP2A. Here, we report that high levels of ZNF512B expression lead to nuclear protein and chromatin aggregation foci that form in a manner that is dependent on the ZF domains of ZNF512B. Notably, we demonstrate ZNF512B binding to the nucleosome remodeling and deacetylase (NuRD) complex. We discover a conserved amino acid sequence within ZNF512B that resembles the NuRD-interaction motif (NIM) previously identified in FOG-1 and other transcriptional regulators. By solving the crystal structure of this motif bound to the NuRD component RBBP4 and by applying several biochemical and biophysical assays, we demonstrate that this internal NIM is both necessary and sufficient for robust and high-affinity NuRD binding. Transcriptome analyses and reporter assays identify ZNF512B as a repressor of gene expression that can act in both NuRD-dependent and -independent ways. Our study might have implications for diseases in which ZNF512B expression is deregulated, such as cancer and neurodegenerative diseases, and hints at the existence of more proteins as potential NuRD interactors.
    DOI:  https://doi.org/10.1093/nar/gkae926
  24. Nat Cancer. 2024 Oct 30.
    Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis.
    Yizhou Zhu, Hayan Lee, Shannon White, Annika K Weimer, Emma Monte, Aaron Horning, Stephanie A Nevins, Edward D Esplin, Kristina Paul, Gat Krieger, Zohar Shipony, Roxanne Chiu, Rozelle Laquindanum, Thomas V Karathanos, Melissa W Y Chua, Meredith Mills, Uri Ladabaum, Teri Longacre, Jeanne Shen, Ariel Jaimovich, Doron Lipson, Anshul Kundaje, William J Greenleaf, Christina Curtis, James M Ford, Michael P Snyder.
      Although three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution chromatin conformation maps of 33 colon samples spanning different stages of early neoplastic growth in persons with familial adenomatous polyposis (FAP). Our analysis revealed a substantial progressive loss of genome-wide cis-regulatory connectivity at early malignancy stages, correlating with nonlinear gene regulation effects. Genes with high promoter-enhancer (P-E) connectivity in unaffected mucosa were not linked to elevated baseline expression but tended to be upregulated in advanced stages. Inhibiting highly connected promoters preferentially represses gene expression in CRC cells compared to normal colonic epithelial cells. Our results suggest a two-phase model whereby neoplastic transformation reduces P-E connectivity from a redundant state to a rate-limiting one for transcriptional levels, highlighting the intricate interplay between 3D genome architecture and gene regulation during early CRC progression.
    DOI:  https://doi.org/10.1038/s43018-024-00823-z
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