bims-ginsta 2024-01-14 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–01–14
thirty-two papers selected by
Jinrong Hu, National University of Singapore

Control of successive unequal cell divisions by neural cell fate regulators determines embryonic neuroblast cell size.
Phosphorylation regulates tau's phase separation behavior and interactions with chromatin.
eIF5A controls mitoprotein import by relieving ribosome stalling at the TIM50 translocase mRNA.
Should I shrink or should I grow: cell size changes in tissue morphogenesis.
Cyclin A/Cdk1 promotes chromosome alignment and timely mitotic progression.
Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair.
Keep quiet: the HUSH complex in transcriptional silencing and disease.
Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate.
RNA polymerases reshape chromatin and coordinate transcription on individual fibers.
The human Y and inactive X chromosomes similarly modulate autosomal gene expression.
F-actin coordinates spindle morphology and function in Drosophila meiosis.
Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism.
Kinome-wide siRNA screen identifies a DCLK2-TBK1 oncogenic signaling axis in clear cell renal cell carcinoma.
Perlecan (HSPG2) promotes structural, contractile, and metabolic development of human cardiomyocytes.
Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells.
Direct observation of a condensate effect on super-enhancer controlled gene bursting.
Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions.
Control of cardiac contractions using Cre-lox and degron strategies in zebrafish.
p53 suppresses lipid droplet-fueled tumorigenesis through phosphatidylcholine.
Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells.
Cell type-specific enrichment of somatic aneuploidy in the mammalian brain.
Structure of a membrane tethering complex incorporating multiple SNAREs.
EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues.
Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes.
A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network.
Juvenile hormones direct primordial germ cell migration to the embryonic gonad.
Liquid-like condensates mediate competition between actin branching and bundling.
Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson's disease model.
A time- and single-cell-resolved model of murine bone marrow hematopoiesis.
On the edge: how nuclear pore complexes rule genome stability.
Control of NAD+ homeostasis by autophagic flux modulates mitochondrial and cardiac function.
Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners.

Development. 2024 01 11. pii: dev.200981. [Epub ahead of print]

Control of successive unequal cell divisions by neural cell fate regulators determines embryonic neuroblast cell size.

T W Mullan, T Felton, J Tam, O Kasem, T J Yeung, N Memar, R Schnabel, R J Poole.

  Asymmetric cell divisions often generate daughter cells of unequal size in addition to different fates. In some contexts, daughter cell size asymmetry is thought to be a key input to specific binary cell fate decisions. An alternative possibility is that unequal division is a mechanism by which a variety of cells of different sizes are generated during embryonic development. We show here that two unequal cell divisions precede neuroblast formation in the C lineage of C. elegans. The equalisation of these divisions in a pig-1/MELK mutant background has little effect on neuroblast specification. Instead, we reveal let-19/MDT13 as a novel regulator of the proneural bHLH transcription factor hlh-14/ASCL1 and find that both are required to concomitantly regulate the acquisition of neuroblast identity and neuroblast cell size. Thus, embryonic neuroblast cell size in this lineage is progressively regulated in parallel with identity by key neural cell fate regulators. We propose that key cell fate determinants have a novel function to regulate unequal cleavage and therefore cell size of the progenitor cells whose daughter cell fates they then go on to specify.

Keywords:   C. elegans ; Asymmetric division; Neuronal specification; Proneural

DOI:  https://doi.org/10.1242/dev.200981
bioRxiv. 2023 Dec 23. pii: 2023.12.21.572911. [Epub ahead of print]

Phosphorylation regulates tau's phase separation behavior and interactions with chromatin.

Lannah S Abasi, Nesreen Elathram, Manasi Movva, Amar Deep, Kevin D Corbett, Galia T Debelouchina.

Tau is a microtubule-associated protein often found in neurofibrillary tangles (NFTs) in the brains of patients with Alzheimer's disease (AD). Beyond this context, mounting evidence suggests that tau localizes into the nucleus, where it may play a role in DNA protection and heterochromatin regulation. Models of tau depletion or pathology show loss of genetically silent heterochromatin, aberrant expression of heterochromatic genes, and transposable element activation. The molecular mechanisms behind these observations are currently unclear. Using in vitro biophysical experiments, here we demonstrate that tau can undergo liquid-liquid phase separation (LLPS) with DNA, mononucleosomes, and reconstituted nucleosome arrays under low salt conditions. Low concentrations of tau promote chromatin compaction and protect DNA from digestion. While the material state of samples at physiological salt is dominated by chromatin oligomerization, tau can still associate strongly and reversibly with nucleosome arrays. These properties are driven by tau's strong interactions with linker and nucleosomal DNA, while magic angle spinning (MAS) solid-state NMR experiments show that tau binding does not drastically alter nucleosome structure and dynamics. In addition, tau co-localizes into droplets formed by nucleosome arrays and phosphorylated HP1α, a key heterochromatin constituent thought to function through an LLPS mechanism. Importantly, LLPS and chromatin interactions are disrupted by aberrant tau hyperphosphorylation. These biophysical properties suggest that tau may directly impact DNA and chromatin accessibility and that loss of these interactions could contribute to the aberrant nuclear effects seen in tau pathology.

DOI: https://doi.org/10.1101/2023.12.21.572911
bioRxiv. 2023 Dec 19. pii: 2023.12.19.572290. [Epub ahead of print]

eIF5A controls mitoprotein import by relieving ribosome stalling at the TIM50 translocase mRNA.

Marina Barba-Aliaga, Vanessa Bernal, Cynthia Rong, Brian M Zid, Paula Alepuz.

The efficient import of nuclear-encoded proteins into mitochondria is crucial for proper mitochondrial function. The conserved translation factor eIF5A is primarily known as an elongation factor which binds ribosomes to alleviate ribosome stalling at sequences encoding polyprolines or combinations of proline with glycine and charged amino acids. eIF5A is known to impact the mitochondrial function across a variety of species although the precise molecular mechanism underlying this impact remains unclear. We found that depletion of eIF5A in yeast drives reduced translation and levels of TCA cycle and oxidative phosphorylation proteins. We further found that loss of eIF5A leads to the accumulation of mitoprotein precursors in the cytosol as well as to the induction of a mitochondrial import stress response. Here we identify an essential polyproline-containing protein as a direct eIF5A target for translation: the mitochondrial inner membrane protein Tim50, which is the receptor sub-unit of the TIM23 translocase complex. We show how eIF5A directly controls mitochondrial protein import through the alleviation of ribosome stalling along TIM50 mRNA at the mitochondrial surface. Removal of the polyprolines from Tim50 rescues the mitochondrial import stress response, as well as the translation of oxidative phosphorylation reporter genes in an eIF5A loss of function. Overall, our findings elucidate how eIF5A impacts the mitochondrial function by reducing ribosome stalling and facilitating protein translation, thereby positively impacting the mitochondrial import process.

DOI: https://doi.org/10.1101/2023.12.19.572290
Genome. 2024 Jan 10.

Should I shrink or should I grow: cell size changes in tissue morphogenesis.

Gordana Scepanovic, Rodrigo Fernandez-Gonzalez.

Cells change shape, move, divide and die to sculpt tissues. Common to all these cell behaviours are cell size changes, which have recently emerged as key contributors to tissue morphogenesis. Cells can change their mass-the number of macromolecules they contain-or their volume-the space they encompass. Changes in cell mass and volume occur through different molecular mechanisms and at different timescales, slow for changes in mass and rapid for changes in volume. Therefore, changes in cell mass and cell volume, which are often linked, contribute to the development and shaping of tissues in different ways. Here, we review the molecular mechanisms by which cells can control and alter their size, and we discuss how changes in cell mass and volume contribute to tissue morphogenesis. The role that cell size control plays in developing embryos is only starting to be elucidated. Research on the signals that control cell size will illuminate our understanding of the cellular and molecular mechanisms that drive tissue morphogenesis.

DOI: https://doi.org/10.1139/gen-2023-0091
bioRxiv. 2023 Dec 21. pii: 2023.12.21.572788. [Epub ahead of print]

Cyclin A/Cdk1 promotes chromosome alignment and timely mitotic progression.

Sarah Y Valles, Kristina M Godek, Duane A Compton.

To ensure genomic fidelity a series of spatially and temporally coordinated events are executed during prometaphase of mitosis, including bipolar spindle formation, chromosome attachment to spindle microtubules at kinetochores, the correction of erroneous kinetochore-microtubule (k-MT) attachments, and chromosome congression to the spindle equator. Cyclin A/Cdk1 kinase plays a key role in destabilizing k-MT attachments during prometaphase to promote correction of erroneous k-MT attachments. However, it is unknown if Cyclin A/Cdk1 kinase regulates other events during prometaphase. Here, we investigate additional roles of Cyclin A/Cdk1 in prometaphase by using an siRNA knockdown strategy to deplete endogenous Cyclin A from human cells. We find that depleting Cyclin A significantly extends mitotic duration, specifically prometaphase, because chromosome alignment is delayed. Unaligned chromosomes display erroneous monotelic, syntelic, or lateral k-MT attachments suggesting that bioriented k-MT attachment formation is delayed in the absence of Cyclin A. Mechanistically, chromosome alignment is likely impaired because the localization of the kinetochore proteins BUB1 kinase, KNL1, and MPS1 kinase are reduced in Cyclin A-depleted cells. Moreover, we find that Cyclin A promotes BUB1 kinetochore localization independently of its role in destabilizing k-MT attachments. Thus, Cyclin A/Cdk1 facilitates chromosome alignment during prometaphase to support timely mitotic progression.

DOI: https://doi.org/10.1101/2023.12.21.572788
Proc Natl Acad Sci U S A. 2024 Jan 16. 121(3): e2314245121

Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair.

Reta D Sarsam, Jun Xu, Indrajit Lahiri, Wenzhi Gong, Qingrong Li, Juntaek Oh, Zhen Zhou, Peini Hou, Jenny Chong, Nan Hao, Shisheng Li, Dong Wang, Andres E Leschziner.

  Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a common mechanism to recognize a stalled Pol II, with additional interactions when Pol II is arrested at a lesion. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces further interactions between Rad26 and a lesion-arrested Pol II. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation. Together, our results provide important mechanistic insights into how two conserved transcription-coupled repair factors, Rad26/CSB and Elf1/ELOF1, work together at the initial lesion recognition steps of transcription-coupled repair.

Keywords:  Cockayne syndrome B; Elf1; RNA polymerase II; cryo-EM; transcription-coupled repair

DOI:  https://doi.org/10.1073/pnas.2314245121
Nat Struct Mol Biol. 2024 Jan 12.

Keep quiet: the HUSH complex in transcriptional silencing and disease.

Iris Müller, Kristian Helin.

The human silencing hub (HUSH) complex is an epigenetic repressor complex whose role has emerged as an important guardian of genome integrity. It protects the genome from exogenous DNA invasion and regulates endogenous retroelements by recruiting histone methyltransferases catalyzing histone 3 lysine 9 trimethylation (H3K9me3) and additional proteins involved in chromatin compaction. In particular, its regulation of transcriptionally active LINE1 retroelements, by binding to and neutralizing LINE1 transcripts, has been well characterized. HUSH is required for mouse embryogenesis and is associated with disease, in particular cancer. Here we provide insights into the structural and biochemical features of the HUSH complex. Furthermore, we discuss the molecular mechanisms by which the HUSH complex is recruited to specific genomic regions and how it silences transcription. Finally, we discuss the role of HUSH complex members in mammalian development, antiretroviral immunity, and diseases such as cancer.

DOI: https://doi.org/10.1038/s41594-023-01173-7
Mol Cell. 2024 Jan 04. pii: S1097-2765(23)01026-2. [Epub ahead of print]

Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate.

Satoshi Matsui, Marissa Granitto, Morgan Buckley, Katie Ludwig, Sandra Koigi, Joseph Shiley, William J Zacharias, Christopher N Mayhew, Hee-Woong Lim, Makiko Iwafuchi.

  Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.

Keywords:  FOXA; NuRD; OCT4; PRC; PRDM1; PRDM14; Polycomb repressive complex; bivalent epigenetic state; cell fate control; complex; nucleosome remodeling and deacetylation; pioneer transcription factor

DOI:  https://doi.org/10.1016/j.molcel.2023.12.007
bioRxiv. 2023 Dec 23. pii: 2023.12.22.573133. [Epub ahead of print]

RNA polymerases reshape chromatin and coordinate transcription on individual fibers.

Thomas W Tullius, R Stefan Isaac, Jane Ranchalis, Danilo Dubocanin, L Stirling Churchman, Andrew B Stergachis.

During eukaryotic transcription, RNA polymerases must initiate and pause within a crowded, complex environment, surrounded by nucleosomes and other transcriptional activity. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address these limitations, we employed long-read chromatin fiber sequencing (Fiber-seq) to visualize RNA polymerases within their native chromatin context at single-molecule and near single-nucleotide resolution along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of single-molecule RNA Polymerase (Pol) II and III transcription associated footprints, which, in aggregate, mirror bulk short-read sequencing-based measurements of transcription. We show that Pol II pausing destabilizes downstream nucleosomes, with frequently paused genes maintaining a short-term memory of these destabilized nucleosomes. Furthermore, we demonstrate pervasive direct coordination and anti-coordination between nearby Pol II genes, Pol III genes, transcribed enhancers, and insulator elements. This coordination is largely limited to spatially organized elements within 5 kb of each other, implicating short-range chromatin environments as a predominant determinant of coordinated polymerase initiation. Overall, transcription initiation reshapes surrounding nucleosome architecture and coordinates nearby transcriptional machinery along individual chromatin fibers.

DOI: https://doi.org/10.1101/2023.12.22.573133
Cell Genom. 2023 Dec 07. pii: S2666-979X(23)00306-3. [Epub ahead of print] 100462

The human Y and inactive X chromosomes similarly modulate autosomal gene expression.

Adrianna K San Roman, Helen Skaletsky, Alexander K Godfrey, Neha V Bokil, Levi Teitz, Isani Singh, Laura V Blanton, Daniel W Bellott, Tatyana Pyntikova, Julian Lange, Natalia Koutseva, Jennifer F Hughes, Laura Brown, Sidaly Phou, Ashley Buscetta, Paul Kruszka, Nicole Banks, Amalia Dutra, Evgenia Pak, Patricia C Lasutschinkow, Colleen Keen, Shanlee M Davis, Angela E Lin, Nicole R Tartaglia, Carole Samango-Sprouse, Maximilian Muenke, David C Page.

  Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.

Keywords:  CRISPR; Klinefelter syndrome; Turner syndrome; X chromosome inactivation; aneuploidy; gene expression; sex chromosomes; sex differences; transcription factors

DOI:  https://doi.org/10.1016/j.xgen.2023.100462
PLoS Genet. 2024 Jan 11. 20(1): e1011111

F-actin coordinates spindle morphology and function in Drosophila meiosis.

Benjamin W Wood, Xingzhu Shi, Timothy T Weil.

Meiosis is a highly conserved feature of sexual reproduction that ensures germ cells have the correct number of chromosomes prior to fertilization. A subset of microtubules, known as the spindle, are essential for accurate chromosome segregation during meiosis. Building evidence in mammalian systems has recently highlighted the unexpected requirement of the actin cytoskeleton in chromosome segregation; a network of spindle actin filaments appear to regulate many aspects of this process. Here we show that Drosophila oocytes also have a spindle population of actin that appears to regulate the formation of the microtubule spindle and chromosomal movements throughout meiosis. We demonstrate that genetic and pharmacological disruption of the actin cytoskeleton has a significant impact on spindle morphology, dynamics, and chromosome alignment and segregation during maturation and the metaphase-anaphase transition. We further reveal a role for calcium in maintaining the microtubule spindle and spindle actin. Together, our data highlights potential conservation of morphology and mechanism of the spindle actin during meiosis.

DOI: https://doi.org/10.1371/journal.pgen.1011111
Cell. 2024 Jan 05. pii: S0092-8674(23)01342-9. [Epub ahead of print]

Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism.

Joshua D Meisel, Maria Miranda, Owen S Skinner, Presli P Wiesenthal, Sandra M Wellner, Alexis A Jourdain, Gary Ruvkun, Vamsi K Mootha.

  The electron transport chain (ETC) of mitochondria, bacteria, and archaea couples electron flow to proton pumping and is adapted to diverse oxygen environments. Remarkably, in mice, neurological disease due to ETC complex I dysfunction is rescued by hypoxia through unknown mechanisms. Here, we show that hypoxia rescue and hyperoxia sensitivity of complex I deficiency are evolutionarily conserved to C. elegans and are specific to mutants that compromise the electron-conducting matrix arm. We show that hypoxia rescue does not involve the hypoxia-inducible factor pathway or attenuation of reactive oxygen species. To discover the mechanism, we use C. elegans genetic screens to identify suppressor mutations in the complex I accessory subunit NDUFA6/nuo-3 that phenocopy hypoxia rescue. We show that NDUFA6/nuo-3(G60D) or hypoxia directly restores complex I forward activity, with downstream rescue of ETC flux and, in some cases, complex I levels. Additional screens identify residues within the ubiquinone binding pocket as being required for the rescue by NDUFA6/nuo-3(G60D) or hypoxia. This reveals oxygen-sensitive coupling between an accessory subunit and the quinone binding pocket of complex I that can restore forward activity in the same manner as hypoxia.

Keywords:  C. elegans; NADH:ubiquinone oxidoreductase; NDUFA6; NDUFS4; complex I; electron transport chain; hyperoxia; hypoxia; mitochondria; oxygen

DOI:  https://doi.org/10.1016/j.cell.2023.12.010
Mol Cell. 2024 Jan 04. pii: S1097-2765(23)01029-8. [Epub ahead of print]

Kinome-wide siRNA screen identifies a DCLK2-TBK1 oncogenic signaling axis in clear cell renal cell carcinoma.

Lianxin Hu, Yanfeng Zhang, Lei Guo, Hua Zhong, Ling Xie, Jin Zhou, Chengheng Liao, Hongwei Yao, Jun Fang, Hongyi Liu, Cheng Zhang, Hui Zhang, Xiaoqiang Zhu, Maowu Luo, Alex von Kriegsheim, Bufan Li, Weibo Luo, Xuewu Zhang, Xian Chen, Joshua T Mendell, Lin Xu, Payal Kapur, Albert S Baldwin, James Brugarolas, Qing Zhang.

  TANK-binding kinase 1 (TBK1) is a potential therapeutic target in multiple cancers, including clear cell renal cell carcinoma (ccRCC). However, targeting TBK1 in clinical practice is challenging. One approach to overcome this challenge would be to identify an upstream TBK1 regulator that could be targeted therapeutically in cancer specifically. In this study, we perform a kinome-wide small interfering RNA (siRNA) screen and identify doublecortin-like kinase 2 (DCLK2) as a TBK1 regulator in ccRCC. DCLK2 binds to and directly phosphorylates TBK1 on Ser172. Depletion of DCLK2 inhibits anchorage-independent colony growth and kidney tumorigenesis in orthotopic xenograft models. Conversely, overexpression of DCLK2203, a short isoform that predominates in ccRCC, promotes ccRCC cell growth and tumorigenesis in vivo. Mechanistically, DCLK2203 elicits its oncogenic signaling via TBK1 phosphorylation and activation. Taken together, these results suggest that DCLK2 is a TBK1 activator and potential therapeutic target for ccRCC.

Keywords:  DCLK2; NMD pathway; TBK1; ccRCC; oncogene

DOI:  https://doi.org/10.1016/j.molcel.2023.12.010
Cell Rep. 2024 Jan 09. pii: S2211-1247(23)01679-0. [Epub ahead of print]43(1): 113668

Perlecan (HSPG2) promotes structural, contractile, and metabolic development of human cardiomyocytes.

Benjamin B Johnson, Marie-Victoire Cosson, Lorenza I Tsansizi, Terri L Holmes, Tegan Gilmore, Katherine Hampton, Ok-Ryul Song, Nguyen T N Vo, Aishah Nasir, Alzbeta Chabronova, Chris Denning, Mandy J Peffers, Catherine L R Merry, John Whitelock, Linda Troeberg, Stuart A Rushworth, Andreia S Bernardo, James G W Smith.

  Perlecan (HSPG2), a heparan sulfate proteoglycan similar to agrin, is key for extracellular matrix (ECM) maturation and stabilization. Although crucial for cardiac development, its role remains elusive. We show that perlecan expression increases as cardiomyocytes mature in vivo and during human pluripotent stem cell differentiation to cardiomyocytes (hPSC-CMs). Perlecan-haploinsuffient hPSCs (HSPG2+/-) differentiate efficiently, but late-stage CMs have structural, contractile, metabolic, and ECM gene dysregulation. In keeping with this, late-stage HSPG2+/- hPSC-CMs have immature features, including reduced ⍺-actinin expression and increased glycolytic metabolism and proliferation. Moreover, perlecan-haploinsuffient engineered heart tissues have reduced tissue thickness and force generation. Conversely, hPSC-CMs grown on a perlecan-peptide substrate are enlarged and display increased nucleation, typical of hypertrophic growth. Together, perlecan appears to play the opposite role of agrin, promoting cellular maturation rather than hyperplasia and proliferation. Perlecan signaling is likely mediated via its binding to the dystroglycan complex. Targeting perlecan-dependent signaling may help reverse the phenotypic switch common to heart failure.

Keywords:  CP: Cell biology; CP: Developmental biology; agrin; cardiac maturation; cardiomyocytes; extracellular matrix; heparan sulfate proteoglycan; human pluripotent stem cells; hypertrophy; multinucleation; perlecan; perlecan mutation

DOI:  https://doi.org/10.1016/j.celrep.2023.113668
Nat Struct Mol Biol. 2024 Jan 09.

Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells.

Almira Chervova, Amandine Molliex, H Irem Baymaz, Rémi-Xavier Coux, Thaleia Papadopoulou, Florian Mueller, Eslande Hercul, David Fournier, Agnès Dubois, Nicolas Gaiani, Petra Beli, Nicola Festuccia, Pablo Navarro.

Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate reactivation after mitotic gene silencing. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the biological significance and importance of their bookmarking function. Here we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover a large redundancy in mitotic binding among members of the protein super-family of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ESRRB is essential in maintaining pluripotency in mouse embryonic stem cells, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly those most efficiently reactivated in G1. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.

DOI: https://doi.org/10.1038/s41594-023-01195-1
Cell. 2023 Dec 29. pii: S0092-8674(23)01337-5. [Epub ahead of print]

Direct observation of a condensate effect on super-enhancer controlled gene bursting.

Manyu Du, Simon Hendrik Stitzinger, Jan-Hendrik Spille, Won-Ki Cho, Choongman Lee, Mohammed Hijaz, Andrea Quintana, Ibrahim I Cissé.

  Enhancers are distal DNA elements believed to loop and contact promoters to control gene expression. Recently, we found diffraction-sized transcriptional condensates at genes controlled by clusters of enhancers (super-enhancers). However, a direct function of endogenous condensates in controlling gene expression remains elusive. Here, we develop live-cell super-resolution and multi-color 3D-imaging approaches to investigate putative roles of endogenous condensates in the regulation of super-enhancer controlled gene Sox2. In contrast to enhancer distance, we find instead that the condensate's positional dynamics are a better predictor of gene expression. A basal gene bursting occurs when the condensate is far (>1 μm), but burst size and frequency are enhanced when the condensate moves in proximity (<1 μm). Perturbations of cohesin and local DNA elements do not prevent basal bursting but affect the condensate and its burst enhancement. We propose a three-way kissing model whereby the condensate interacts transiently with gene locus and regulatory DNA elements to control gene bursting.

Keywords:  RNA polymerase II; Sox2; biomolecular condensate; cluster; cohesin; function; nuclear organization; phase separation; super-enhancer; transcription

DOI:  https://doi.org/10.1016/j.cell.2023.12.005
bioRxiv. 2023 Dec 20. pii: 2023.12.20.572584. [Epub ahead of print]

Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions.

Laila Karra, Anna-Marie Finger, Lauren Shechtman, Milana Krush, Rita Meng-Yao Huang, Morgan Prinz, Iliana Tennvooren, Kriti Bahl, Lisiena Hysienaj, Paulina G Gonzalez, Alexis J Combes, Hugo Gonzalez, Rafael J Argüello, Matthew H Spitzer, Jeroen P Roose.

Normal hematopoiesis requires constant prolific production of different blood cell lineages by multipotent hematopoietic stem cells (HSC). Stem- and progenitor- cells need to balance dormancy with proliferation. How genetic alterations impact frequency, lineage potential, and metabolism of HSC is largely unknown. Here, we compared induced expression of KRAS G12D or RasGRP1 to normal hematopoiesis. At low-resolution, both Ras pathway lesions result in skewing towards myeloid lineages. Single-cell resolution CyTOF proteomics unmasked an expansion of HSC- and progenitor- compartments for RasGRP1, contrasted by a depletion for KRAS G12D . SCENITH™ quantitates protein synthesis with single-cell precision and corroborated that immature cells display low metabolic SCENITH™ rates. Both RasGRP1 and KRAS G12D elevated mean SCENITH™ signals in immature cells. However, RasGRP1-overexpressing stem cells retain a metabolically quiescent cell-fraction, whereas this fraction diminishes for KRAS G12D . Our temporal single cell proteomics and metabolomics datasets provide a resource of mechanistic insights into altered hematopoiesis at single cell resolution.

DOI: https://doi.org/10.1101/2023.12.20.572584
Proc Natl Acad Sci U S A. 2024 Jan 16. 121(3): e2309842121

Control of cardiac contractions using Cre-lox and degron strategies in zebrafish.

Thomas Juan, Maëlle Bellec, Bárbara Cardoso, Héloïse Athéa, Nana Fukuda, Marga Albu, Stefan Günther, Mario Looso, Didier Y R Stainier.

  Cardiac contractions and hemodynamic forces are essential for organ development and homeostasis. Control over cardiac contractions can be achieved pharmacologically or optogenetically. However, these approaches lack specificity or require direct access to the heart. Here, we compare two genetic approaches to control cardiac contractions by modulating the levels of the essential sarcomeric protein Tnnt2a in zebrafish. We first recombine a newly generated tnnt2a floxed allele using multiple lines expressing Cre under the control of cardiomyocyte-specific promoters, and show that it does not recapitulate the tnnt2a/silent heart mutant phenotype in embryos. We show that this lack of early cardiac contraction defects is due, at least in part, to the long half-life of tnnt2a mRNA, which masks the gene deletion effects until the early larval stages. We then generate an endogenous Tnnt2a-eGFP fusion line that we use together with the zGRAD system to efficiently degrade Tnnt2a in all cardiomyocytes. Using single-cell transcriptomics, we find that Tnnt2a depletion leads to cardiac phenotypes similar to those observed in tnnt2a mutants, with a loss of blood and pericardial flow-dependent cell types. Furthermore, we achieve conditional degradation of Tnnt2a-eGFP by splitting the zGRAD protein into two fragments that, when combined with the cpFRB2-FKBP system, can be reassembled upon rapamycin treatment. Thus, this Tnnt2a degradation line enables non-invasive control of cardiac contractions with high spatial and temporal specificity and will help further understand how they shape organ development and homeostasis.

Keywords:  Cre-lox; Degron; cardiac contractions; cardiac troponin T; cpFRB2-FKBP

DOI:  https://doi.org/10.1073/pnas.2309842121
J Clin Invest. 2024 Jan 09. pii: e171788. [Epub ahead of print]

p53 suppresses lipid droplet-fueled tumorigenesis through phosphatidylcholine.

Xiuduan Xu, Jianqin Wang, Li Xu, Peng Li, Peng Jiang.

  Choline deficiency causes disorders including hepatic abnormalities and is associated with an increased risk of multiple types of cancer(1, 2). Here, by choline free diet-associated RNA-seq analyses, we found that the tumor suppressor p53 drives the Kennedy pathway via PCYT1B to control the growth of lipid droplets (LDs) and their fueling role in tumorigenesis. Mechanistically, through upregulation of PCYT1B, p53 channeled depleted choline stores to phosphatidylcholine (PC) biosynthesis during choline starvation, thus preventing LD coalescence. Cells lacking p53 failed to complete this response to choline depletion, leading to hepatic steatosis and tumorigenesis, and these effects could be reversed by enforcing PCYT1B expression or restoring PC abundance. Furthermore, loss of p53 or defects in the Kennedy pathway increased surface localization of hormone-sensitive lipase (HSL) on LDs to release specific fatty acids that fueled tumor cells in vivo and in vitro. Thus, p53 loss leads to dysregulation of choline metabolism and LD growth, and couples perturbed LD homeostasis to tumorigenesis.

Keywords:  Cancer; Cell Biology; Cholesterol; Tumor suppressors

DOI:  https://doi.org/10.1172/JCI171788
Cell Rep. 2024 Jan 08. pii: S2211-1247(23)01675-3. [Epub ahead of print]43(1): 113664

Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells.

Matthew M Edwards, Ning Wang, Dashiell J Massey, Sakshi Bhatele, Dieter Egli, Amnon Koren.

  Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.

Keywords:  CP: Molecular biology; CP: Stem cell research; DNA replication timing; epigenetic aberrations; heterochromatin; induced pluripotent stem cells; somatic cell nuclear transfer; stem cell differentiation

DOI:  https://doi.org/10.1016/j.celrep.2023.113664
bioRxiv. 2023 Dec 19. pii: 2023.12.18.572285. [Epub ahead of print]

Cell type-specific enrichment of somatic aneuploidy in the mammalian brain.

Eran A Mukamel, Hanqing Liu, M Margarita Behrens, Joseph R Ecker.

Somatic mutations alter the genomes of a subset of an individual's brain cells1-3, impacting gene regulation and contributing to disease processes4,5. Mosaic single nucleotide variants have been characterized with single-cell resolution in the brain2,3, but we have limited information about large-scale structural variation, including whole-chromosome duplication or loss1,6,7. We used a dataset of over 415,000 single-cell DNA methylation and chromatin conformation profiles across the adult mouse brain to identify aneuploid cells comprehensively. Whole-chromosome loss or duplication occurred in <1% of cells, with rates up to 1.8% in non-neuronal cell types, including oligodendrocyte precursors and pericytes. Among all aneuploidies, we observed a strong enrichment of trisomy on chromosome 16, which is syntenic with human chromosome 21 and constitutively trisomic in Down syndrome. Chromosome 16 trisomy occurred in multiple cell types and across brain regions, suggesting that nondisjunction is a recurrent feature of somatic variation in the brain.

DOI: https://doi.org/10.1101/2023.12.18.572285
Nat Struct Mol Biol. 2024 Jan 09.

Structure of a membrane tethering complex incorporating multiple SNAREs.

Kevin A DAmico, Abigail E Stanton, Jaden D Shirkey, Sophie M Travis, Philip D Jeffrey, Frederick M Hughson.

Most membrane fusion reactions in eukaryotic cells are mediated by multisubunit tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial attachment of two membranes. Complementary SNAREs then form membrane-bridging complexes whose assembly draws the membranes together for fusion. Here we present a cryo-electron microscopy structure of the simplest known MTC, the 255-kDa Dsl1 complex of Saccharomyces cerevisiae, bound to the two SNAREs that anchor it to the endoplasmic reticulum. N-terminal domains of the SNAREs form an integral part of the structure, stabilizing a Dsl1 complex configuration with unexpected similarities to the 850-kDa exocyst MTC. The structure of the SNARE-anchored Dsl1 complex and its comparison with exocyst reveal what are likely to be common principles underlying MTC function. Our structure also implies that tethers and SNAREs can work together as a single integrated machine.

DOI: https://doi.org/10.1038/s41594-023-01164-8
bioRxiv. 2023 Dec 22. pii: 2023.12.22.573057. [Epub ahead of print]

EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues.

D Nathaniel Clarke, Adam C Martin.

The movements that give rise to the body's structure are powered by cell shape changes and rearrangements that are coordinated at supracellular scales. How such cellular coordination arises and integrates different morphogenetic programs is unclear. Using quantitative imaging, we found a complex pattern of adherens junction (AJ) levels in the ectoderm prior to gastrulation onset in Drosophila. AJ intensity exhibited a double-sided gradient, with peaks at the dorsal midline and ventral neuroectoderm. We show that this dorsal-ventral AJ pattern is regulated by epidermal growth factor (EGF) signaling and that this signal is required for ectoderm cell movement during mesoderm invagination and axis extension. We identify AJ levels and junctional actomyosin as downstream effectors of EGFR signaling. Overall, our study demonstrates a mechanism of coordination between tissue folding and convergent extension that facilitates embryo-wide gastrulation movements.

DOI: https://doi.org/10.1101/2023.12.22.573057
bioRxiv. 2023 Dec 23. pii: 2023.12.21.572835. [Epub ahead of print]

Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes.

James R Simmons, Brandon Estrem, Maxim V Zagoskin, Ryan Oldridge, Sobhan Bahrami Zadegan, Jianbin Wang.

  A growing list of metazoans undergo programmed DNA elimination (PDE), where a significant amount of DNA is selectively lost from the somatic genome during development. In some nematodes, PDE leads to the removal and remodeling of the ends of all germline chromosomes. In several species, PDE also generates internal breaks that lead to sequence loss and an increased number of somatic chromosomes. The biological significance of these karyotype changes associated with PDE and the origin and evolution of nematode PDE remain largely unknown. Here, we assembled the single germline chromosome of the horse parasite Parascaris univalens and compared the karyotypes, chromosomal gene organization, and PDE features among ascarid nematodes. We show that PDE in Parascaris converts an XX/XY sex-determination system in the germline into an XX/XO system in the somatic cells. Comparisons of Ascaris, Parascaris, and Baylisascaris ascarid chromosomes suggest that PDE existed in the ancestor of these parasites, and their current distinct germline karyotypes were derived from fusion events of smaller ancestral chromosomes. The DNA breaks involved in PDE resolve these fused germline chromosomes into their pre-fusion karyotypes, leading to alterations in genome architecture and gene expression in the somatic cells. Cytological and genomic analyses further suggest that satellite DNA and the heterochromatic chromosome arms play a dynamic role in the Parascaris germline chromosome during meiosis. Overall, our results show that chromosome fusion and PDE have been harnessed in these ascarids to sculpt their karyotypes, altering the genome organization and serving specific functions in the germline and somatic cells.

Keywords:  DNA break; Parascaris; centromere; chromosome fusion; genome; karyotype; meiosis; nematode; programmed DNA elimination; satellite DNA

DOI:  https://doi.org/10.1101/2023.12.21.572835
Circulation. 2024 Jan 08.

A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network.

Michael T Broman, Rangarajan D Nadadur, Carlos Perez-Cervantes, Ozanna Burnicka-Turek, Sonja Lazarevic, Anna Gams, Brigitte Laforest, Jeffrey D Steimle, Sabrina Iddir, Zhezhen Wang, Linsin Smith, Stefan R Mazurek, Harold E Olivey, Pingzhu Zhou, Margaret Gadek, Kaitlyn M Shen, Zoheb Khan, Joshua W M Theisen, Xinan H Yang, Kohta Ikegami, Igor R Efimov, William T Pu, Christopher R Weber, Elizabeth M McNally, Eric C Svensson, Ivan P Moskowitz.

   BACKGROUND: The relationship between heart failure (HF) and atrial fibrillation (AF) is clear, with up to half of patients with HF progressing to AF. The pathophysiological basis of AF in the context of HF is presumed to result from atrial remodeling. Upregulation of the transcription factor FOG2 (friend of GATA2; encoded by ZFPM2) is observed in human ventricles during HF and causes HF in mice.
METHODS: FOG2 expression was assessed in human atria. The effect of adult-specific FOG2 overexpression in the mouse heart was evaluated by whole animal electrophysiology, in vivo organ electrophysiology, cellular electrophysiology, calcium flux, mouse genetic interactions, gene expression, and genomic function, including a novel approach for defining functional transcription factor interactions based on overlapping effects on enhancer noncoding transcription.
RESULTS: FOG2 is significantly upregulated in the human atria during HF. Adult cardiomyocyte-specific FOG2 overexpression in mice caused primary spontaneous AF before the development of HF or atrial remodeling. FOG2 overexpression generated arrhythmia substrate and trigger in cardiomyocytes, including calcium cycling defects. We found that FOG2 repressed atrial gene expression promoted by TBX5. FOG2 bound a subset of GATA4 and TBX5 co-bound genomic locations, defining a shared atrial gene regulatory network. FOG2 repressed TBX5-dependent transcription from a subset of co-bound enhancers, including a conserved enhancer at the Atp2a2 locus. Atrial rhythm abnormalities in mice caused by Tbx5 haploinsufficiency were rescued by Fog2 haploinsufficiency.
CONCLUSIONS: Transcriptional changes in the atria observed in human HF directly antagonize the atrial rhythm gene regulatory network, providing a genomic link between HF and AF risk independent of atrial remodeling.

Keywords:  RNA; RNA, long noncoding; RNA, untranslated; atrial fibrillation; calcium signaling; gene regulatory networks; heart failure

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.123.066804
Curr Biol. 2024 Jan 08. pii: S0960-9822(23)01733-5. [Epub ahead of print]

Juvenile hormones direct primordial germ cell migration to the embryonic gonad.

Lacy J Barton, Justina Sanny, Emily Packard Dawson, Marcela Nouzova, Fernando Gabriel Noriega, Matthias Stadtfeld, Ruth Lehmann.

  Germ cells are essential to sexual reproduction. Across the animal kingdom, extracellular signaling isoprenoids, such as retinoic acids (RAs) in vertebrates and juvenile hormones (JHs) in invertebrates, facilitate multiple processes in reproduction. Here we investigated the role of these potent signaling molecules in embryonic germ cell development, using JHs in Drosophila melanogaster as a model system. In contrast to their established endocrine roles during larval and adult germline development, we found that JH signaling acts locally during embryonic development. Using an in vivo biosensor, we observed active JH signaling first within and near primordial germ cells (PGCs) as they migrate to the developing gonad. Through in vivo and in vitro assays, we determined that JHs are both necessary and sufficient for PGC migration. Analysis into the mechanisms of this newly uncovered paracrine JH function revealed that PGC migration was compromised when JHs were decreased or increased, suggesting that specific titers or spatiotemporal JH dynamics are required for robust PGC colonization of the gonad. Compromised PGC migration can impair fertility and cause germ cell tumors in many species, including humans. In mammals, retinoids have many roles in development and reproduction. We found that like JHs in Drosophila, RA was sufficient to impact mouse PGC migration in vitro. Together, our study reveals a previously unanticipated role of isoprenoids as local effectors of pre-gonadal PGC development and suggests a broadly shared mechanism in PGC migration.

Keywords:  Hmgcr; cell movement; embryonic development; gametogenesis; germ cells; gonad; juvenile hormones; ovary; retinoids; testis

DOI:  https://doi.org/10.1016/j.cub.2023.12.033
Proc Natl Acad Sci U S A. 2024 Jan 16. 121(3): e2309152121

Liquid-like condensates mediate competition between actin branching and bundling.

Kristin Graham, Aravind Chandrasekaran, Liping Wang, Noel Yang, Eileen M Lafer, Padmini Rangamani, Jeanne C Stachowiak.

  Cellular remodeling of actin networks underlies cell motility during key morphological events, from embryogenesis to metastasis. In these transformations, there is an inherent competition between actin branching and bundling, because steric clashes among branches create a mechanical barrier to bundling. Recently, liquid-like condensates consisting purely of proteins involved in either branching or bundling of the cytoskeleton have been found to catalyze their respective functions. Yet in the cell, proteins that drive branching and bundling are present simultaneously. In this complex environment, which factors determine whether a condensate drives filaments to branch or become bundled? To answer this question, we added the branched actin nucleator, Arp2/3, to condensates composed of VASP, an actin bundling protein. At low actin to VASP ratios, branching activity, mediated by Arp2/3, robustly inhibited VASP-mediated bundling of filaments, in agreement with agent-based simulations. In contrast, as the actin to VASP ratio increased, addition of Arp2/3 led to formation of aster-shaped structures, in which bundled filaments emerged from a branched actin core, analogous to filopodia emerging from a branched lamellipodial network. These results demonstrate that multi-component, liquid-like condensates can modulate the inherent competition between bundled and branched actin morphologies, leading to organized, higher-order structures, similar to those found in motile cells.

Keywords:  actin; biomechanics; biomolecular condensate; cytoskeleton; liquid–liquid phase separation

DOI:  https://doi.org/10.1073/pnas.2309152121
Nat Commun. 2024 Jan 10. 15(1): 447

Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson's disease model.

Gustavo Morrone Parfitt, Elena Coccia, Camille Goldman, Kristen Whitney, Ricardo Reyes, Lily Sarrafha, Ki Hong Nam, Soha Sohail, Drew R Jones, John F Crary, Alban Ordureau, Joel Blanchard, Tim Ahfeldt.

Accumulation of advanced glycation end products (AGEs) on biopolymers accompanies cellular aging and drives poorly understood disease processes. Here, we studied how AGEs contribute to development of early onset Parkinson's Disease (PD) caused by loss-of-function of DJ1, a protein deglycase. In induced pluripotent stem cell (iPSC)-derived midbrain organoid models deficient for DJ1 activity, we find that lysosomal proteolysis is impaired, causing AGEs to accumulate, α-synuclein (α-syn) phosphorylation to increase, and proteins to aggregate. We demonstrated these processes are at least partly driven by astrocytes, as DJ1 loss reduces their capacity to provide metabolic support and triggers acquisition of a pro-inflammatory phenotype. Consistently, in co-cultures, we find that DJ1-expressing astrocytes are able to reverse the proteolysis deficits of DJ1 knockout midbrain neurons. In conclusion, astrocytes' capacity to clear toxic damaged proteins is critical to preserve neuronal function and their dysfunction contributes to the neurodegeneration observed in a DJ1 loss-of-function PD model.

DOI: https://doi.org/10.1038/s41467-024-44732-2
Cell Stem Cell. 2023 Dec 29. pii: S1934-5909(23)00431-9. [Epub ahead of print]

A time- and single-cell-resolved model of murine bone marrow hematopoiesis.

Iwo Kucinski, Joana Campos, Melania Barile, Francesco Severi, Natacha Bohin, Pedro N Moreira, Lewis Allen, Hannah Lawson, Myriam L R Haltalli, Sarah J Kinston, Dónal O'Carroll, Kamil R Kranc, Berthold Göttgens.

  The paradigmatic hematopoietic tree model is increasingly recognized to be limited, as it is based on heterogeneous populations largely defined by non-homeostatic assays testing cell fate potentials. Here, we combine persistent labeling with time-series single-cell RNA sequencing to build a real-time, quantitative model of in vivo tissue dynamics for murine bone marrow hematopoiesis. We couple cascading single-cell expression patterns with dynamic changes in differentiation and growth speeds. The resulting explicit linkage between molecular states and cellular behavior reveals widely varying self-renewal and differentiation properties across distinct lineages. Transplanted stem cells show strong acceleration of differentiation at specific stages of erythroid and neutrophil production, illustrating how the model can quantify the impact of perturbations. Our reconstruction of dynamic behavior from snapshot measurements is akin to how a kinetoscope allows sequential images to merge into a movie. We posit that this approach is generally applicable to understanding tissue-scale dynamics at high resolution.

Keywords:  Hoxb5; differentiation rate; dynamics; hematopoiesis; modeling; progenitors; scRNA-seq; self-renewal; stem cells

DOI:  https://doi.org/10.1016/j.stem.2023.12.001
Curr Opin Genet Dev. 2024 Jan 11. pii: S0959-437X(23)00130-2. [Epub ahead of print]84 102150

On the edge: how nuclear pore complexes rule genome stability.

Marie-Noëlle Simon, Karine Dubrana, Benoit Palancade.

Nuclear organization has emerged as a critical layer in the coordination of DNA repair activities. Distinct types of DNA lesions have notably been shown to relocate at the vicinity of nuclear pore complexes (NPCs), where specific repair pathways are favored, ultimately safeguarding genome integrity. Here, we review the most recent progress in this field, notably highlighting the increasingly diverse types of DNA structures undergoing repositioning, and the signaling pathways involved. We further discuss our growing knowledge of the molecular mechanisms underlying the choice of repair pathways at NPCs, and their conservation - or divergences. Intriguingly, a series of recent findings suggest that DNA metabolism may be coupled to NPC biogenesis and specialization, challenging our initial vision of these processes.

DOI: https://doi.org/10.1016/j.gde.2023.102150
EMBO J. 2024 Jan 11.

Control of NAD+ homeostasis by autophagic flux modulates mitochondrial and cardiac function.

Quanjiang Zhang, Zhonggang Li, Qiuxia Li, Samuel Aj Trammell, Mark S Schmidt, Karla Maria Pires, Jinjin Cai, Yuan Zhang, Helena Kenny, Sihem Boudina, Charles Brenner, E Dale Abel.

  Impaired autophagy is known to cause mitochondrial dysfunction and heart failure, in part due to altered mitophagy and protein quality control. However, whether additional mechanisms are involved in the development of mitochondrial dysfunction and heart failure in the setting of deficient autophagic flux remains poorly explored. Here, we show that impaired autophagic flux reduces nicotinamide adenine dinucleotide (NAD+) availability in cardiomyocytes. NAD+ deficiency upon autophagic impairment is attributable to the induction of nicotinamide N-methyltransferase (NNMT), which methylates the NAD+ precursor nicotinamide (NAM) to generate N-methyl-nicotinamide (MeNAM). The administration of nicotinamide mononucleotide (NMN) or inhibition of NNMT activity in autophagy-deficient hearts and cardiomyocytes restores NAD+ levels and ameliorates cardiac and mitochondrial dysfunction. Mechanistically, autophagic inhibition causes the accumulation of SQSTM1, which activates NF-κB signaling and promotes NNMT transcription. In summary, we describe a novel mechanism illustrating how autophagic flux maintains mitochondrial and cardiac function by mediating SQSTM1-NF-κB-NNMT signaling and controlling the cellular levels of NAD+.

Keywords:  Autophagic Flux; Heart Dysfunction; Mitochondrial Homeostasis; NAD+ Metabolism

DOI:  https://doi.org/10.1038/s44318-023-00009-w
Nat Commun. 2024 Jan 11. 15(1): 473

Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners.

Pankaj Sharma, Elena Maklashina, Markus Voehler, Sona Balintova, Sarka Dvorakova, Michal Kraus, Katerina Hadrava Vanova, Zuzana Nahacka, Renata Zobalova, Stepana Boukalova, Kristyna Cunatova, Tomas Mracek, Hans K Ghayee, Karel Pacak, Jakub Rohlena, Jiri Neuzil, Gary Cecchini, T M Iverson.

Complex II (CII) activity controls phenomena that require crosstalk between metabolism and signaling, including neurodegeneration, cancer metabolism, immune activation, and ischemia-reperfusion injury. CII activity can be regulated at the level of assembly, a process that leverages metastable assembly intermediates. The nature of these intermediates and how CII subunits transfer between metastable complexes remains unclear. In this work, we identify metastable species containing the SDHA subunit and its assembly factors, and we assign a preferred temporal sequence of appearance of these species during CII assembly. Structures of two species show that the assembly factors undergo disordered-to-ordered transitions without the appearance of significant secondary structure. The findings identify that intrinsically disordered regions are critical in regulating CII assembly, an observation that has implications for the control of assembly in other biomolecular complexes.

DOI: https://doi.org/10.1038/s41467-023-44563-7