RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription [Research Papers]
Promoter-proximal RNA Pol II pausing is a critical step in transcriptional control. Pol II pausing has been predominantly studied in tissue culture systems. While Pol II pausing has been shown to be required for mammalian development, the phenotypic and mechanistic details of this requirement are unknown. Here, we found that loss of Pol II pausing stalls pluripotent state transitions within the epiblast of the early mouse embryo. Using Nelfb–/– mice and a NELFB degron mouse pluripotent stem cell model, we show that embryonic stem cells (ESCs) representing the naïve state of pluripotency successfully ini...
Source: Genes and Development - September 1, 2022 Category: Genetics & Stem Cells Authors: Abuhashem, A., Chivu, A. G., Zhao, Y., Rice, E. J., Siepel, A., Danko, C. G., Hadjantonakis, A.-K. Tags: Research Papers Source Type: research
The dual nature of the nucleolus [Perspectives]
The nucleolus is best known for housing the highly ordered assembly line that produces ribosomal subunits. The >100 ribosome assembly factors in the nucleolus are thought to cycle between two states: an operative state (when integrated into subunit assembly intermediates) and a latent state (upon release from intermediates). Although it has become commonplace to refer to the nucleolus as "being a multilayered condensate," and this may be accurate for latent factors, there is little reason to think that such assertions pertain to the operative state of assembly factors. (Source: Genes and Development)
Source: Genes and Development - September 1, 2022 Category: Genetics & Stem Cells Authors: Tartakoff, A., DiMario, P., Hurt, E., McStay, B., Panse, V. G., Tollervey, D. Tags: Translation, Chromosome Dynamics and Nuclear Architecture, Post-transcriptional Control Perspectives Source Type: research
Histone methyltransferase DOT1L is essential for self-renewal of germline stem cells [Research Papers]
Self-renewal of spermatogonial stem cells is vital to lifelong production of male gametes and thus fertility. However, the underlying mechanisms remain enigmatic. Here, we show that DOT1L, the sole H3K79 methyltransferase, is required for spermatogonial stem cell self-renewal. Mice lacking DOT1L fail to maintain spermatogonial stem cells, characterized by a sequential loss of germ cells from spermatogonia to spermatids and ultimately a Sertoli cell only syndrome. Inhibition of DOT1L reduces the stem cell activity after transplantation. DOT1L promotes expression of the fate-determining HoxC transcription factors in spermato...
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Lin, H., Cheng, K., Kubota, H., Lan, Y., Riedel, S. S., Kakiuchi, K., Sasaki, K., Bernt, K. M., Bartolomei, M. S., Luo, M., Wang, P. J. Tags: Research Papers Source Type: research
Primary cilia control translation and the cell cycle in medulloblastoma [Research Papers]
The primary cilium, a signaling organelle projecting from the surface of a cell, controls cellular physiology and behavior. The presence or absence of primary cilia is a distinctive feature of a given tumor type; however, whether and how the primary cilium contributes to tumorigenesis are unknown for most tumors. Medulloblastoma (MB) is a common pediatric brain cancer comprising four groups: SHH, WNT, group 3 (G3), and group 4 (G4). From 111 cases of MB, we show that primary cilia are abundant in SHH and WNT MBs but rare in G3 and G4 MBs. Using WNT and G3 MB mouse models, we show that primary cilia promote WNT MB by facili...
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Youn, Y. H., Hou, S., Wu, C.-C., Kawauchi, D., Orr, B. A., Robinson, G. W., Finkelstein, D., Taketo, M. M., Gilbertson, R. J., Roussel, M. F., Han, Y.-G. Tags: Research Papers Source Type: research
Upstream open reading frames control PLK4 translation and centriole duplication in primordial germ cells [Research Papers]
Centrosomes are microtubule-organizing centers comprised of a pair of centrioles and the surrounding pericentriolar material. Abnormalities in centriole number are associated with cell division errors and can contribute to diseases such as cancer. Centriole duplication is limited to once per cell cycle and is controlled by the dosage-sensitive Polo-like kinase 4 (PLK4). Here, we show that PLK4 abundance is translationally controlled through conserved upstream open reading frames (uORFs) in the 5' UTR of the mRNA. Plk4 uORFs suppress Plk4 translation and prevent excess protein synthesis. Mice with homozygous knockout of Plk...
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Phan, T. P., Boatwright, C. A., Drown, C. G., Skinner, M. W., Strong, M. A., Jordan, P. W., Holland, A. J. Tags: Research Papers Source Type: research
Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus [Research Papers]
How distal regulatory elements control gene transcription and chromatin topology is not clearly defined, yet these processes are closely linked in lineage specification during development. Through allele-specific genome editing and chromatin interaction analyses of the Sox2 locus in mouse embryonic stem cells, we found a striking disconnection between transcriptional control and chromatin architecture. We traced nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletions have no effect on promoter–enhancer interaction frequencies or topological domain organi...
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Taylor, T., Sikorska, N., Shchuka, V. M., Chahar, S., Ji, C., Macpherson, N. N., Moorthy, S. D., de Kort, M. A. C., Mullany, S., Khader, N., Gillespie, Z. E., Langroudi, L., Tobias, I. C., Lenstra, T. L., Mitchell, J. A., Sexton, T. Tags: Research Papers Source Type: research
Cell and chromatin transitions in intestinal stem cell regeneration [Research Papers]
The progeny of intestinal stem cells (ISCs) dedifferentiate in response to ISC attrition. The precise cell sources, transitional states, and chromatin remodeling behind this activity remain unclear. In the skin, stem cell recovery after injury preserves an epigenetic memory of the damage response; whether similar memories arise and persist in regenerated ISCs is not known. We addressed these questions by examining gene activity and open chromatin at the resolution of single Neurog3-labeled mouse intestinal crypt cells, hence deconstructing forward and reverse differentiation of the intestinal secretory (Sec) lineage. We sh...
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Singh, P. N. P., Madha, S., Leiter, A. B., Shivdasani, R. A. Tags: Research Papers Source Type: research
Recurrent chromosomal translocations in sarcomas create a megacomplex that mislocalizes NuA4/TIP60 to Polycomb target loci [Research Papers]
In this study, we characterize the fusion protein produced by the EPC1-PHF1 translocation. The chimeric protein assembles a megacomplex harboring both NuA4/TIP60 and PRC2 activities and leads to mislocalization of chromatin marks in the genome, in particular over an entire topologically associating domain including part of the HOXD cluster. This is linked to aberrant gene expression—most notably increased expression of PRC2 target genes. Furthermore, we show that JAZF1—implicated with a PRC2 component in the most frequent translocation in ESSs, JAZF1-SUZ12—is a potent transcription activator that physical...
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Sudarshan, D., Avvakumov, N., Lalonde, M.-E., Alerasool, N., Joly-Beauparlant, C., Jacquet, K., Mameri, A., Lambert, J.-P., Rousseau, J., Lachance, C., Paquet, E., Herrmann, L., Thonta Setty, S., Loehr, J., Bernardini, M. Q., Rouzbahman, M., Gingras, A.-C Tags: Research Papers Source Type: research
Modeling congenital heart disease: lessons from mice, hPSC-based models, and organoids [Reviews]
Congenital heart defects (CHDs) are among the most common birth defects, but their etiology has long been mysterious. In recent decades, the development of a variety of experimental models has led to a greater understanding of the molecular basis of CHDs. In this review, we contrast mouse models of CHD, which maintain the anatomical arrangement of the heart, and human cellular models of CHD, which are more likely to capture human-specific biology but lack anatomical structure. We also discuss the recent development of cardiac organoids, which are a promising step toward more anatomically informative human models of CHD. (S...
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Rao, K. S., Kameswaran, V., Bruneau, B. G. Tags: Development, Cancer and Disease Models Reviews Source Type: research
Subgroup-specific roles of primary cilia in medulloblastoma [Outlook]
Here I discuss the study in this issue of Genes & Development by Youn et al. (pp. 737–751), which describes defined and diverse roles of primary cilia in molecularly distinct medulloblastoma subgroups, highlighting once again the importance of designing subgroup-specific therapeutic approaches for this tumor. (Source: Genes and Development)
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Marino, S. Tags: Cell Cycle and DNA Replication Outlook Source Type: research
Balancing the scales: fine-tuning Polo-like kinase 4 to ensure proper centriole duplication [Outlook]
Polo-like kinase 4 (Plk4) is the master regulator of centriole assembly. Several evolutionarily conserved mechanisms strictly regulate Plk4 abundance and activity to ensure cells maintain a proper number of centrioles. In this issue of Genes & Development, Phan et al. (pp. 718–736) add to this growing list by describing a new mechanism of control that restricts Plk4 translation through competitive ribosome binding at upstream open reading frames (uORFs) in the mature Plk4 mRNA. Fascinatingly, this mechanism is especially critical in the development of primordial germ cells in mice that are transcriptionally hyper...
Source: Genes and Development - July 14, 2022 Category: Genetics & Stem Cells Authors: Ryniawec, J. M., Rogers, G. C. Tags: Stem & Progenitor Cells, Cell Cycle and DNA Replication Outlook Source Type: research
The SpoVA membrane complex is required for dipicolinic acid import during sporulation and export during germination [Research Papers]
In response to starvation, endospore-forming bacteria differentiate into stress-resistant spores that can remain dormant for years yet rapidly germinate and resume growth in response to nutrients. The small molecule dipicolinic acid (DPA) plays a central role in both the stress resistance of the dormant spore and its exit from dormancy during germination. The spoVA locus is required for DPA import during sporulation and has been implicated in its export during germination, but the molecular bases are unclear. Here, we define the minimal set of proteins encoded in the Bacillus subtilis spoVA operon required for DPA import a...
Source: Genes and Development - June 9, 2022 Category: Genetics & Stem Cells Authors: Gao, Y., Barajas-Ornelas, R. D. C., Amon, J. D., Ramirez-Guadiana, F. H., Alon, A., Brock, K. P., Marks, D. S., Kruse, A. C., Rudner, D. Z. Tags: Research Papers Source Type: research
ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD [Research Papers]
DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA, which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question, we performed biochemical, cellular, and structural studies. We show ...
Source: Genes and Development - June 9, 2022 Category: Genetics & Stem Cells Authors: Gozzi, K., Salinas, R., Nguyen, V. D., Laub, M. T., Schumacher, M. A. Tags: Research Papers Source Type: research
Multiomics analysis of the NAD+-PARP1 axis reveals a role for site-specific ADP-ribosylation in splicing in embryonic stem cells [Research Papers]
The differentiation of embryonic stem cells (ESCs) into a lineage-committed state is a dynamic process involving changes in cellular metabolism, epigenetic modifications, post-translational modifications, gene expression, and RNA processing. Here we integrated data from metabolomic, proteomic, and transcriptomic assays to characterize how alterations in NAD+ metabolism during the differentiation of mouse ESCs lead to alteration of the PARP1-mediated ADP-ribosylated (ADPRylated) proteome and mRNA isoform specialization. Our metabolomic analyses indicate that mESCs use distinct NAD+ biosynthetic pathways in different cell st...
Source: Genes and Development - June 9, 2022 Category: Genetics & Stem Cells Authors: Jones, A., Kraus, W. L. Tags: Research Papers Source Type: research
The microRNA-183/96/182 cluster inhibits lung cancer progression and metastasis by inducing an interleukin-2-mediated antitumor CD8+ cytotoxic T-cell response [Research Papers]
One of the mechanisms by which cancer cells acquire hyperinvasive and migratory properties with progressive loss of epithelial markers is the epithelial-to-mesenchymal transition (EMT). We have previously reported that in different cancer types, including nonsmall cell lung cancer (NSCLC), the microRNA-183/96/182 cluster (m96cl) is highly repressed in cells that have undergone EMT. In the present study, we used a novel conditional m96cl mouse to establish that loss of m96cl accelerated the growth of Kras mutant autochthonous lung adenocarcinomas. In contrast, ectopic expression of the m96cl in NSCLC cells results in a robu...
Source: Genes and Development - June 9, 2022 Category: Genetics & Stem Cells Authors: Kundu, S. T., Rodriguez, B. L., Gibson, L. A., Warner, A. N., Perez, M. G., Bajaj, R., Fradette, J. J., Class, C. A., Solis, L. M., Rojas Alvarez, F. R., Wistuba, I. I., Diao, L., Chen, F., Sachdeva, M., Wang, J., Kirsch, D. G., Creighton, C. J., Gibbons, Tags: Research Papers Source Type: research
