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Articles by Alexander Polyzos
T follicular helper cells transiently unlock a plasticity state in germinal centre B cells during the humoral immune response - Nature Cell Biology
Abstract During the germinal centre (GC) reaction, mature B cells undergo rapid and reversible phenotypic shifts that are essential for adaptive immunity. Here we report that GC B cells, unlike other mature B cells, transiently acquire a unique epigenetic plasticity, demonstrated by their enhanced capacity to reprogram to induced pluripotent stem cells. This plasticity depends on T follicular helper (TFH) cells and is not due to increased proliferation or MYC activation.
Disruption of TAD hierarchy promotes LTR co-option in cancer - Nature Genetics
Abstract Transposable elements (TEs) are abundant in the human genome, and they provide the source for genetic and functional diversity. Previous studies have suggested that TEs are repressed by DNA methylation and chromatin modifications. Here through integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters (altPs) at the long terminal repeats (LTRs) of the TE subclasses.
Three-dimensional regulatory hubs support oncogenic programs in glioblastoma
Keywords glioblastoma 3D chromatin organization enhancer-promoter interactions enhancer hubs clonogenicity oncogenic program structural variants HiChIP single-cell RNA-seq CRISPRi regulatory hubs Get full text access Log in, subscribe or purchase for full access. References 1. Brennan, C.W. ∙ Verhaak, R.G.W. ∙ McKenna, A. ... The somatic genomic landscape of glioblastoma Cell. 2013; 155:462-477 2. Stupp, R. ∙ Mason, W.P. ∙ van den Bent, M.J. ...
Single-cell analysis of bidirectional reprogramming between early embryonic states identify mechanisms of differential lineage plasticities in mice
Keywords epiblast primitive endoderm ES cells XEN cells pluripotency extra-embryonic endoderm reprogramming lineage plasticity single-cell analysis blastocyst Get full text access Log in, subscribe or purchase for full access. References 1. Chazaud, C. ∙ Yamanaka, Y. Lineage specification in the mouse preimplantation embryo Development. 2016; 143:1063-1074 2. Schrode, N. ∙ Xenopoulos, P. ∙ Piliszek, A. ...
An Unbiased Approach to Identifying Cellular Reprogramming-Inducible Enhancers
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An Unbiased Approach to Identify Cellular Reprogramming Inducible Enhancers
Preprint Article Version 1 This version is not peer-reviewed Version 1 : Received: 30 October 2024 / Approved: 31 October 2024 / Online: 31 October 2024 (10:38:11 CET) Klagkou, E.; Valakos, D.; Foutadakis, S.; Polyzos, A.; Papadopoulou, A.; Vatsellas, G.; Thanos, D. An Unbiased Approach to Identify Cellular Reprogramming Inducible Enhancers. Preprints 2024, 2024102527.
H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization
Abramo K. Valton A.-L. Venev S.V. Ozadam H. Fox A.N. Dekker J. A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. Nat. Cell Biol. 2019; 21: 1393-1402 Alipour E. Marko J.F. Self-organization of domain structures by DNA-loop-extruding enzymes. Nucleic Acids Res. 2012; 40: 11202-11212 Anders S. Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010; 11: R106 Anders S. Pyl P.T. Huber W.
Context-Dependent Requirement of Euchromatic Histone Methyltransferase Activity during Reprogramming to Pluripotency
Highlights • EHMT function during mouse cell reprogramming is modulated by ascorbic acid (AA) • EHMT inhibition counteracts reprogramming in the presence of AA • EHMT inhibition in the presence of AA results in global erasure of H3K9 dimethylation • Cells reprogrammed in the presence of EHMT inhibitor are functionally impaired Summary Methylation of histone 3 at lysine 9 (H3K9) constitutes a roadblock for cellular reprogramming.
KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks
Abstract Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors, as is exemplified by reprogramming somatic cells to pluripotent stem cells through the expression of OCT4, KLF4, SOX2 and cMYC. How transcription factors orchestrate the complex molecular changes around their target gene loci remains incompletely understood.
Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability
Protein extraction and cell fractionation were performed as described before [9]. Thirty micrograms of protein from total extracts per sample were adjusted with Laemmli buffer (Sigma) and loaded on acrylamide/bis-acrylamide gels. Gel electrophoresis, transfer to PVDF membrane (Millipore), and signal development with nitro blue tetrazolium/5-bromo-4-chloro-3-indolylphosphate (NBT/BCIP) solution (Molecular Probes) or chemiluminescence were performed as previously described [9].
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