Biology subjects

Katznelson, A.

Publications and source records attributed to Katznelson, A..

3 recordsLinked to original sources

bioRxiv2024

Heterochromatin protein ERH represses alternative cell fates during early mammalian differentiation

Enhancer of Rudimentary Homolog (ERH) is an evolutionarily conserved protein originally characterized as promoting fission yeast heterochromatin1 and recently shown to maintain H3K9me3 heterochromatin in human fibroblasts2. Here, we find that ERH depletion in fibroblasts reverts the somatic cell H3K9me3 landscape of broad megabase size domains to an embryonic stem cell (ESC) state composed of mainly H3K9me3 peaks and enables activation of naive and pluripotency genes and transposable elements during induced pluripotent stem cell (iPSC) reprogramming. Concordantly, we find that ERH represses totipotent and alternative lineage programs during mouse preimplantation development and is required for proper segregation of the inner cell mass and trophectoderm cell lineages. During human ESC differentiation into germ layer lineages, ERH silences naive and pluripotency genes, transposable elements, and alternative lineage somatic genes. As in fission yeast, we find that mammalian ERH interacts with RNA-binding proteins to engage and repress its chromatin targets. Our findings reveal a conserved, fundamental role for ERH in cell fate specification via the initiation and maintenance of early developmental gene repression.

developmental biology↗

bioRxiv2023

Physiological reprogramming in vivo mediated by Sox4 pioneer factor activity

Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cells enhancers. Here we report that Sox4 is sufficient to initiate hepatobiliary metaplasia in the adult liver. In lineage-traced cells, we assessed the timing of Sox4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, Sox4 directly binds to and closes hepatocyte regulatory sequences via a motif it overlaps with Hnf4a, a hepatocyte master regulator. Subsequently, Sox4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.

cell biology↗

bioRxiv2022

Distinct Chromatin Scanning Modes Lead to Targeting of Compacted Chromatin by Pioneer Factors FOXA1 and SOX2

Pioneer transcription factors, by interacting with nucleosomes, can scan silent, compact chromatin to target gene regulatory sequences, enabling cooperative binding events that modulate local chromatin structure and gene activity. However, pioneer factors do not target all of their cognate motifs and it is unclear whether different pioneers scan compact chromatin the same way. Surprisingly, combined approaches of genomics and single-molecule tracking show that to target DNase-resistant, low-histone turnover sites, pioneer factors can use opposite dynamics of chromatin scanning. FOXA1 uses low nucleoplasmic diffusion and stable chromatin interactions, whereas SOX2 uses high nucleoplasmic diffusion and transient interactions, respectively. Despite such differences, FOXA1 and SOX2 scan low-mobility, silent chromatin to similar extents, as mediated by protein domains outside of the respective DNA binding domains. By contrast, the non-pioneer HNF4A predominantly targets DNase-sensitive, nucleosome-depleted regions. We conclude that the targeting of compact chromatin sites by pioneer factors can be through distinct dynamic processes.

molecular biology↗