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What are tethering elements?
Curr Opin Genet Dev. 2024 Feb;84:102151. doi: 10.1016/j.gde.2023.102151. Epub 2024 Jan 18.ABSTRACTHigh-resolution Micro-C maps identified a specialized class of regulatory DNAs termed 'tethering elements' (TEs) in Drosophila. These 300-500-bp elements facilitate specific long-range genomic associations or loops. The POZ-containing transcription factor GAF (GAGA-associated factor) contributes to loop formation. Tether-tether interactions accelerate Hox gene activation by distal enhancers, and coordinate transcription of duplicated genes (paralogs) through promoter-promoter associations. Some TEs engage in ultra-long-range e...
Source: Current Opinion in Genetics and Development - January 18, 2024 Category: Genetics & Stem Cells Authors: Xiao Li Michael Levine Source Type: research

On the edge: how nuclear pore complexes rule genome stability
Curr Opin Genet Dev. 2024 Feb;84:102150. doi: 10.1016/j.gde.2023.102150. Epub 2024 Jan 12.ABSTRACTNuclear 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 o...
Source: Current Opinion in Genetics and Development - January 12, 2024 Category: Genetics & Stem Cells Authors: Marie-No ëlle Simon Karine Dubrana Benoit Palancade Source Type: research

The stem cell zoo for comparative studies of developmental tempo
Curr Opin Genet Dev. 2024 Feb;84:102149. doi: 10.1016/j.gde.2023.102149. Epub 2024 Jan 9.ABSTRACTThe rate of development is highly variable across animal species. However, the mechanisms regulating developmental tempo have remained elusive due to difficulties in performing direct interspecies comparisons. Here, we discuss how pluripotent stem cell-based models of development can be used to investigate cell- and tissue-autonomous temporal processes. These systems enable quantitative comparisons of different animal species under similar experimental conditions. Moreover, the constantly growing stem cell zoo collection allows...
Source: Current Opinion in Genetics and Development - January 10, 2024 Category: Genetics & Stem Cells Authors: Jorge L ázaro Jaroslaw Sochacki Miki Ebisuya Source Type: research

Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation
Curr Opin Genet Dev. 2024 Feb;84:102147. doi: 10.1016/j.gde.2023.102147. Epub 2024 Jan 4.ABSTRACTDNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on pl...
Source: Current Opinion in Genetics and Development - January 4, 2024 Category: Genetics & Stem Cells Authors: Guanghui Xu Julie A Law Source Type: research

Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation
Curr Opin Genet Dev. 2024 Jan 3;84:102147. doi: 10.1016/j.gde.2023.102147. Online ahead of print.ABSTRACTDNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primari...
Source: Current Opinion in Genetics and Development - January 4, 2024 Category: Genetics & Stem Cells Authors: Guanghui Xu Julie A Law Source Type: research

Deciphering microglia phenotypes in health and disease
Curr Opin Genet Dev. 2024 Jan 2;84:102146. doi: 10.1016/j.gde.2023.102146. Online ahead of print.ABSTRACTMicroglia are the major immune cells of the central nervous system (CNS) that perform numerous adaptive functions required for normal CNS development and homeostasis but are also linked to neurodegenerative and behavioral diseases. Microglia development and function are strongly influenced by brain environmental signals that are integrated at the level of transcriptional enhancers to drive specific programs of gene expression. Here, we describe a conceptual framework for how lineage-determining and signal-dependent tran...
Source: Current Opinion in Genetics and Development - January 3, 2024 Category: Genetics & Stem Cells Authors: Christopher D Balak Claudia Z Han Christopher K Glass Source Type: research

Exploring new roles for RNA-binding proteins in epigenetic and gene regulation
We describe advances in methodologies that define the RNA-protein interactome and machine-learning algorithms that are streamlining RBP discovery and predicting new RNA-binding regions. Finally, we present how RBP dysregulation leads to alterations in tumor-promoting gene expression and discuss the potential for targeting these RBPs for the development of new cancer therapeutics.PMID:38128453 | DOI:10.1016/j.gde.2023.102136 (Source: Current Opinion in Genetics and Development)
Source: Current Opinion in Genetics and Development - December 21, 2023 Category: Genetics & Stem Cells Authors: Pedro Avila-Lopez Shannon M Lauberth Source Type: research