Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells DOI Creative Commons
Nicholas M. Adams, Aleksandra A. Galitsyna, Ioanna Tiniakou

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 22, 2024

Abstract The cohesin protein complex extrudes chromatin loops, stopping at CTCF-bound sites, to organize chromosomes into topologically associated domains, yet the biological implications of this process are poorly understood. We show that is required for post-mitotic differentiation and function antigen-presenting dendritic cells (DCs), particularly antigen cross-presentation IL-12 secretion by type 1 conventional DCs (cDC1s) in vivo . organization was shaped DC-specifying transcription factor IRF8, which controlled looping chromosome compartmentalization, respectively. Notably, optimal expression IRF8 itself CTCF/cohesin-binding sites demarcating Irf8 gene. During DC activation, induction a subset genes with distal enhancers. Accordingly, deletion CTCF flanking Il12b gene reduced production cDC1s. Our data reveal an essential role cohesin-mediated regulation cell , its bi-directional crosstalk lineage-specifying factors.

Language: Английский

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data DOI Creative Commons
Nikki Bialy, Frank Alber, Brenda Andrews

et al.

arXiv (Cornell University), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance scientific understanding complex cellular systems advance predictive personalized therapeutic products for human health. For this potential be realized, quality-assured image data must shared among labs at a global scale compared, pooled, reanalyzed, thus unleashing untold beyond original purpose which was generated. There are two broad sets requirements enable sharing in life sciences. One set is articulated companion White Paper entitled Enabling Global Image Data Sharing Life Sciences, published parallel addresses need build cyberinfrastructure digital array data. In Paper, we detail requirements, involves collecting, managing, presenting, propagating contextual information essential assess quality, understand content, interpret implications, reuse context experimental details. We start by providing an overview main lessons learned date through international community activities, have recently made considerable progress toward generating standard practices imaging Quality Control (QC) metadata. then provide clear recommendations amplifying work. The driving goal address remaining challenges democratize access everyday tools spectrum biomedical researchers, regardless their expertise, resources, geographical location.

Language: Английский

Citations

2
Jupyter Scatter: Interactive Exploration of Large-Scale Datasets DOI Creative Commons
Fritz Lekschas, Trevor Manz

The Journal of Open Source Software, Journal Year: 2024, Volume and Issue: 9(101), P. 7059 - 7059

Published: Sept. 10, 2024

Language: Английский

Citations

2
Epigenetics and the timing of neuronal differentiation DOI
Andrew Aldridge, Anne E. West

Current Opinion in Neurobiology, Journal Year: 2024, Volume and Issue: 89, P. 102915 - 102915

Published: Sept. 14, 2024

Language: Английский

Citations

2
Identifying genetic variants associated with chromatin looping and genome function DOI Creative Commons
Sourya Bhattacharyya, Ferhat Ay

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 18, 2024

Abstract Here we present a comprehensive HiChIP dataset on naïve CD4 T cells (nCD4) from 30 donors and identify QTLs that associate with genotype-dependent and/or allele-specific variation of contacts defining loops between active regulatory regions (iQTLs). We observe substantial overlap iQTLs previously defined eQTLs histone QTLs, an enrichment for fine-mapped GWAS variants. Furthermore, describe distinct subset nCD4 iQTLs, which the significant chromatin in are translated into eQTL trends cell memory subsets. Finally, define connectivity-QTLs as significantly associated concordant changes over broad genomic region (e.g., SNP RNASET2 locus). Our results demonstrate importance complementary modality QTL mapping their power identifying uncharacterized linked to cell-specific gene expression connectivity.

Language: Английский

Citations

2
Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells DOI Creative Commons
Nicholas M. Adams, Aleksandra A. Galitsyna, Ioanna Tiniakou

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 22, 2024

Abstract The cohesin protein complex extrudes chromatin loops, stopping at CTCF-bound sites, to organize chromosomes into topologically associated domains, yet the biological implications of this process are poorly understood. We show that is required for post-mitotic differentiation and function antigen-presenting dendritic cells (DCs), particularly antigen cross-presentation IL-12 secretion by type 1 conventional DCs (cDC1s) in vivo . organization was shaped DC-specifying transcription factor IRF8, which controlled looping chromosome compartmentalization, respectively. Notably, optimal expression IRF8 itself CTCF/cohesin-binding sites demarcating Irf8 gene. During DC activation, induction a subset genes with distal enhancers. Accordingly, deletion CTCF flanking Il12b gene reduced production cDC1s. Our data reveal an essential role cohesin-mediated regulation cell , its bi-directional crosstalk lineage-specifying factors.

Language: Английский

Citations

2