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Publications in Chromatin by NOMIS researchers

Lifelong persistence of nuclear RNAs in the mouse brain

NOMIS Researcher(s)

Published in

April 4, 2024

Genomic DNA that resides in the nuclei of mammalian neurons can be as old as the organism itself. The life span of nuclear RNAs, which are critical for proper chromatin architecture and transcription regulation, has not been determined in adult tissues. In this work, we identified and characterized nuclear RNAs that do not turn over for at least 2 years in a subset of postnatally born cells in the mouse brain. These long-lived RNAs were stably retained in nuclei in a neural cell type–specific manner and were required for the maintenance of heterochromatin. Thus, the life span of neural cells may depend on both the molecular longevity of DNA for the storage of genetic information and also the extreme stability of RNA for the functional organization of chromatin.

Research field(s)
Genetics & Heredity, Biology

DOI
10.1126/science.adf3481

Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

NOMIS Researcher(s)

Published in

June 29, 2023

Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression. © 2023 American Association for the Advancement of Science. All rights reserved.

Research field(s)
Health Sciences, Biomedical Research, Developmental Biology

DOI
10.1126/science.adf5568

Why the Pictorial Needs the Motoric

NOMIS Researcher(s)

Published in

April 20, 2021

Does action play any crucial role in our perception of pictures? The standard literature on picture perception has never explicitly tackled this question. This is for a simple reason. After all, objects in a picture seem to be static objects of perception. Thus, it might sound extremely controversial to say that action is crucial in picture perception. Contrary to this general intuitive stance, this paper defends, for the first time, the apparently very controversial claim, never addressed in the literature, that some of the specific and essential relations between vision and action make action (and its motoric basis) crucial in order for us to enter pictorial experience. I first discuss two ways in which vision and action are deeply linked, by describing the famous notions of Vision-for-Action and Sensorimotor Understanding. Then, I describe the special role they play in generating ordinary pictorial experience and suggest that, when we cannot rely on them while in front of a picture, we lose pictorial experience. © 2021, The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.

Research field(s)
Arts & Humanities

DOI
10.1007/s10670-021-00381-1

Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation

NOMIS Researcher(s)

Published in

July 1, 2020

During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division.

Research field(s)
Health Sciences, Biomedical Research, Developmental Biology

DOI
10.1101/GAD.335794.119

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  • 2024 NOMIS Foundation