Xist nucleates local protein gradients to propagate silencing across the X chromosome

Yolanda Markaki; Johnny Gan Chong; Yuying Wang; Elsie C Jacobson; Christy Luong; Shawn Y X Tan; Joanna W Jachowicz; Mackenzie Strehle; Davide Maestrini; Abhik K Banerjee; Bhaven A Mistry; Iris Dror; Francois Dossin; Johannes Schöneberg; Edith Heard; Mitchell Guttman; Tom Chou; Kathrin Plath

doi:10.1016/j.cell.2021.10.022

Xist nucleates local protein gradients to propagate silencing across the X chromosome

Cell. 2021 Dec 9;184(25):6174-6192.e32. doi: 10.1016/j.cell.2021.10.022. Epub 2021 Nov 4.

Authors

Yolanda Markaki¹, Johnny Gan Chong², Yuying Wang², Elsie C Jacobson², Christy Luong², Shawn Y X Tan², Joanna W Jachowicz³, Mackenzie Strehle³, Davide Maestrini⁴, Abhik K Banerjee³, Bhaven A Mistry⁵, Iris Dror², Francois Dossin⁶, Johannes Schöneberg⁷, Edith Heard⁶, Mitchell Guttman³, Tom Chou⁸, Kathrin Plath⁹

Affiliations

¹ Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: gmarkaki@mednet.ucla.edu.
² Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
³ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
⁴ Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁵ Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Claremont McKenna College, Claremont, CA 91711, USA.
⁶ European Molecular Biology Laboratory, Director's Unit, Heidelberg 69117, Germany.
⁷ Departments of Pharmacology & Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093, USA.
⁸ Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: tomchou@ucla.edu.
⁹ Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: kplath@mednet.ucla.edu.

Abstract

The lncRNA Xist forms ∼50 diffraction-limited foci to transcriptionally silence one X chromosome. How this small number of RNA foci and interacting proteins regulate a much larger number of X-linked genes is unknown. We show that Xist foci are locally confined, contain ∼2 RNA molecules, and nucleate supramolecular complexes (SMACs) that include many copies of the critical silencing protein SPEN. Aggregation and exchange of SMAC proteins generate local protein gradients that regulate broad, proximal chromatin regions. Partitioning of numerous SPEN molecules into SMACs is mediated by their intrinsically disordered regions and essential for transcriptional repression. Polycomb deposition via SMACs induces chromatin compaction and the increase in SMACs density around genes, which propagates silencing across the X chromosome. Our findings introduce a mechanism for functional nuclear compartmentalization whereby crowding of transcriptional and architectural regulators enables the silencing of many target genes by few RNA molecules.

Keywords: RNA-binding proteins; X chromosome inactivation; Xist RNA; biomolecular condensates; chromatin organization; heterochromatin; macromolecular dynamics; quantitative imaging; super-resolution microscopy; supramolecular complexes.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Apoptosis Regulatory Proteins / metabolism*
Cell Line
Embryonic Stem Cells
Fibroblasts
Gene Silencing
Humans
Mice
Mitochondrial Proteins / metabolism*
Protein Binding
RNA, Long Noncoding / metabolism*
X Chromosome / metabolism*
X Chromosome Inactivation

Substances

Apoptosis Regulatory Proteins
DIABLO protein, human
Mitochondrial Proteins
RNA, Long Noncoding
XIST non-coding RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding