The enhancer module of Integrator controls cell identity and early neural fate commitment

  • Taverna, E., Gotz, M. & Huttner, W. B. The cell biology of neurogenesis: toward an understanding of the development and evolution of the neocortex. Annu. Rev. Cell Dev. Biol. 30, 465–502 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fish, J. L., Dehay, C., Kennedy, H. & Huttner, W. B. Making bigger brains—the evolution of neural-progenitor-cell division. J. Cell Sci. 121, 2783–2793 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nehme, R. et al. Combining NGN2 programming with developmental patterning generates human excitatory neurons with NMDAR-mediated synaptic transmission. Cell Rep. 23, 2509–2523 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Qi, Y. et al. Combined small-molecule inhibition accelerates the derivation of functional cortical neurons from human pluripotent stem cells. Nat. Biotechnol. 35, 154–163 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tchieu, J. et al. A modular platform for differentiation of human PSCs into all major ectodermal lineages. Cell Stem Cell 21, 399–410.e7 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yao, B. et al. Epigenetic mechanisms in neurogenesis. Nat. Rev. Neurosci. 17, 537–549 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cholewa-Waclaw, J. et al. The role of epigenetic mechanisms in the regulation of gene expression in the nervous system. J. Neurosci. 36, 11427–11434 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bergsland, M. et al. Sequentially acting Sox transcription factors in neural lineage development. Genes Dev. 25, 2453–2464 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wapinski, O. L. et al. Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons. Cell 155, 621–635 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Singh, N. P. et al. Genome-wide binding analyses of HOXB1 revealed a novel DNA binding motif associated with gene repression. J. Dev. Biol. 9, 6 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ortabozkoyun, H. et al. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nat. Genet. 54, 202–212 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, Z. et al. Zic2 is an enhancer-binding factor required for embryonic stem cell specification. Mol. Cell 57, 685–694 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hahn, M. A. et al. Reprogramming of DNA methylation at NEUROD2-bound sequences during cortical neuron differentiation. Sci. Adv. 5, eaax0080 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Welsh, S. A. & Gardini, A. Genomic regulation of transcription and RNA processing by the multitasking Integrator complex. Nat. Rev. Mol. Cell Biol. 24, 204–220 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Offley, S. R. et al. A combinatorial approach to uncover an additional Integrator subunit. Cell Rep. 42, 112244 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lai, F., Gardini, A., Zhang, A. & Shiekhattar, R. Integrator mediates the biogenesis of enhancer RNAs. Nature 525, 399–403 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Elrod, N. D. et al. The Integrator complex attenuates promoter-proximal transcription at protein-coding genes. Mol. Cell 76, 738–752.e7 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tatomer, D. C. et al. The Integrator complex cleaves nascent mRNAs to attenuate transcription. Genes Dev. 33, 1525–1538 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Beckedorff, F. et al. The human Integrator complex facilitates transcriptional elongation by endonucleolytic cleavage of nascent transcripts. Cell Rep. 32, 107917 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fianu, I. et al. Structural basis of Integrator-dependent RNA polymerase II termination. Nature 629, 219–227 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vervoort, S. J. et al. The PP2A–Integrator–CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer. Cell 184, 3143–3162.e32 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zheng, H. et al. Identification of Integrator–PP2A complex (INTAC), an RNA polymerase II phosphatase. Science 370, eabb5872 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huang, K. L. et al. Integrator recruits protein phosphatase 2A to prevent pause release and facilitate transcription termination. Mol. Cell 80, 345–358.e9 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barbieri, E. et al. Targeted enhancer activation by a subunit of the Integrator complex. Mol. Cell 71, 103–116.e7 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xu, C. et al. R-loop-dependent promoter-proximal termination ensures genome stability. Nature 621, 610–619 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Oegema, R. et al. Human mutations in integrator complex subunits link transcriptome integrity to brain development. PLoS Genet. 13, e1006809 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Krall, M. et al. Biallelic sequence variants in INTS1 in patients with developmental delays, cataracts, and craniofacial anomalies. Eur. J. Hum. Genet. 27, 582–593 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tepe, B. et al. Bi-allelic variants in INTS11 are associated with a complex neurological disorder. Am. J. Hum. Genet. 110, 774–789 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mascibroda, L. G. et al. INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex. Nat. Commun. 13, 6054 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Graham, V., Khudyakov, J., Ellis, P. & Pevny, L. SOX2 functions to maintain neural progenitor identity. Neuron 39, 749–765 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Favaro, R. et al. Hippocampal development and neural stem cell maintenance require Sox2-dependent regulation of Shh. Nat. Neurosci. 12, 1248–1256 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bertolini, J. A. et al. Mapping the global chromatin connectivity network for Sox2 function in neural stem cell maintenance. Cell Stem Cell 24, 462–476.e6 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wei, C. L., Nicolis, S. K., Zhu, Y. & Pagin, M. Sox2-dependent 3D chromatin interactomes in transcription, neural stem cell proliferation and neurodevelopmental diseases. J. Exp. Neurosci. 13, 1179069519868224 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, X. et al. Biallelic INTS1 mutations cause a rare neurodevelopmental disorder in two chinese siblings. J. Mol. Neurosci. 70, 1–8 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Sabath, K. et al. INTS10–INTS13–INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module. Nat. Commun. 11, 3422 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kovalevich, J. & Langford, D. Considerations for the use of SH-SY5Y neuroblastoma cells in neurobiology. Methods Mol. Biol. 1078, 9–21 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Razew, M., Fraudeau, A., Pfleiderer, M. M., Linares, R. & Galej, W. P. Structural basis of the Integrator complex assembly and association with transcription factors. Mol. Cell 84, 2542–2552.e5 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fan, P. et al. Catalytic-independent functions of INTAC in conferring sensitivity to BET inhibition. Preprint at bioRxiv https://doi.org/10.1101/2024.02.07.579305 (2024).

  • Sabath, K. et al. Basis of gene-specific transcription regulation by the Integrator complex. Mol. Cell 84, 2525–2541.e12 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zucco, A. J. et al. Neural progenitors derived from tuberous sclerosis complex patients exhibit attenuated PI3K/AKT signaling and delayed neuronal differentiation. Mol. Cell Neurosci. 92, 149–163 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, J. E. Basic helix–loop–helix genes in neural development. Curr. Opin. Neurobiol. 7, 13–20 (1997).

    Article 
    PubMed 

    Google Scholar
     

  • Suter, D. M., Tirefort, D., Julien, S. & Krause, K. H. A Sox1 to Pax6 switch drives neuroectoderm to radial glia progression during differentiation of mouse embryonic stem cells. Stem Cells 27, 49–58 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zuniga, A. et al. Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev. 18, 1553–1564 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Conway, S. J. et al. The role of periostin in tissue remodeling across health and disease. Cell. Mol. Life Sci. 71, 1279–1288 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ricard-Blum, S. The collagen family. Cold Spring Harb. Perspect. Biol. 3, a004978 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wei, S. C. et al. Matrix stiffness drives epithelial–mesenchymal transition and tumour metastasis through a TWIST1–G3BP2 mechanotransduction pathway. Nat. Cell Biol. 17, 678–688 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cano, A. et al. The transcription factor snail controls epithelial–mesenchymal transitions by repressing E-cadherin expression. Nat. Cell Biol. 2, 76–83 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Donato, R. et al. Differential development of neuronal physiological responsiveness in two human neural stem cell lines. BMC Neurosci. 8, 36 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sarkar, A. & Hochedlinger, K. The Sox family of transcription factors: versatile regulators of stem and progenitor cell fate. Cell Stem Cell 12, 15–30 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shaulian, E. & Karin, M. AP-1 as a regulator of cell life and death. Nat. Cell Biol. 4, E131–E136 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ameyar, M., Wisniewska, M. & Weitzman, J. B. A role for AP-1 in apoptosis: the case for and against. Biochimie 85, 747–752 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Baillat, D. et al. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 123, 265–276 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fianu, I. et al. Structural basis of Integrator-mediated transcription regulation. Science 374, 883–887 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, H. et al. H3K4me3 regulates RNA polymerase II promoter-proximal pause-release. Nature 615, 339–348 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stein, C. B. et al. Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci. Mol. Cell 82, 4232–4245.e11 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hata, T. & Nakayama, M. Targeted disruption of the murine large nuclear KIAA1440/Ints1 protein causes growth arrest in early blastocyst stage embryos and eventual apoptotic cell death. Biochim. Biophys. Acta 1773, 1039–1051 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Van den Berg, D. L. C. et al. Nipbl interacts with Zfp609 and the Integrator complex to regulate cortical neuron migration. Neuron 93, 348–361 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, Y. et al. The Integrator complex prevents dedifferentiation of intermediate neural progenitors back into neural stem cells. Cell Rep. 27, 987–996.e3 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Miller, A. et al. Sall4 controls differentiation of pluripotent cells independently of the nucleosome remodelling and deacetylation (NuRD) complex. Development 143, 3074–3084 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kosho, T., Okamoto, N. & Coffin-Siris Syndrome International, C. Genotype–phenotype correlation of Coffin–Siris syndrome caused by mutations in SMARCB1, SMARCA4, SMARCE1, and ARID1A. Am. J. Med. Genet. C Semin. Med. Genet. 166, 262–275 (2014).

    Article 
    CAS 

    Google Scholar
     

  • Jung, Y. L., Hung, C., Choi, J., Lee, E. A. & Bodamer, O. Characterizing the molecular impact of KMT2D variants on the epigenetic and transcriptional landscapes in Kabuki syndrome. Hum. Mol. Genet. 32, 2251–2261 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gao, F. et al. Heterozygous mutations in SMARCA2 reprogram the enhancer landscape by global retargeting of SMARCA4. Mol. Cell 75, 891–904.e7 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gabriele, M. et al. YY1 haploinsufficiency causes an intellectual disability syndrome featuring transcriptional and chromatin dysfunction. Am. J. Hum. Genet. 100, 907–925 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zaugg, J. B. et al. Current challenges in understanding the role of enhancers in disease. Nat. Struct. Mol. Biol. 29, 1148–1158 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Harada, T., Morooka, T., Ogawa, S. & Nishida, E. ERK induces p35, a neuron-specific activator of Cdk5, through induction of Egr1. Nat. Cell Biol. 3, 453–459 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Knapska, E. & Kaczmarek, L. A gene for neuronal plasticity in the mammalian brain: Zif268/Egr-1/NGFI-A/Krox-24/TIS8/ZENK? Prog. Neurobiol. 74, 183–211 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sun, Z. et al. EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity. Nat. Commun. 10, 3892 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jia, P. et al. ZMYND8 mediated liquid condensates spatiotemporally decommission the latent super-enhancers during macrophage polarization. Nat. Commun. 12, 6535 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cimadamore, F., Amador-Arjona, A., Chen, C., Huang, C. T. & Terskikh, A. V.SOX2–LIN28/let-7 pathway regulates proliferation and neurogenesis in neural precursors. Proc. Natl Acad. Sci. USA 110, E3017–E3026 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Amador-Arjona, A. et al. SOX2 primes the epigenetic landscape in neural precursors enabling proper gene activation during hippocampal neurogenesis. Proc. Natl Acad. Sci. USA 112, E1936–E1945 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Soufi, A. et al. Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell 161, 555–568 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Soufi, A., Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151, 994–1004 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, C. & Okayama, H. High-efficiency transformation of mammalian cells by plasmid DNA. Mol. Cell. Biol. 7, 2745–2752 (1987).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kolberg, L., Raudvere, U., Kuzmin, I., Vilo, J. & Peterson, H. gprofiler2—an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Res 9, ELIXIR-709 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, T. et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb.) 2, 100141 (2021).

    CAS 
    PubMed 

    Google Scholar
     

  • Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ramirez, F. et al. deepTools2: A next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381–386 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aran, D. et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat. Immunol. 20, 163–172 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burke, E. E. et al. Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs. Nat. Commun. 11, 462 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar