CTCF supports preferentially short lamina-associated domains

Area of Science:

• Chromatin Biology
• Epigenetics
• Genomics

Background:

• Over one-third of the mammalian genome, organized into lamina-associated domains (LADs), interacts with the nuclear lamina.
• LADs are crucial for gene regulation, DNA replication, and repair, with their nuclear envelope association mediated by membrane proteins and border-binding factors.
• CCCTC-binding factor (CTCF) and YY1 are implicated in tethering LADs to the nuclear envelope via their border-binding roles, though this remains unproven genome-wide.

Purpose of the Study:

• To investigate the role of CTCF in maintaining the lamina-associated domain (LAD) landscape using a genome-wide approach.
• To determine if CTCF is essential for LAD association with the nuclear lamina, particularly under conditions of induced chromatin stress.

Main Methods:

• CRISPR-Cas9 was employed to generate melanoma cells with partial loss-of-function (pLoF) of CTCF.
• Lamina-associated domain (LAD) landscape was analyzed using lamin B ChIP-seq in CTCF pLoF cells.
• Chromatin stress was induced by inhibiting RNA polymerase II to assess CTCF's role under duress.

Main Results:

• Under normal conditions, CTCF pLoF caused minor alterations in the LAD landscape (2% increase, 8% decrease).
• Chromatin stress significantly impacted LADs in CTCF pLoF cells, causing 7% to dissociate from the nuclear lamina.
• Dissociated LADs were shorter, enriched for CTCF binding at their borders, and characterized by facultative chromatin status.

Conclusions:

• CTCF plays a critical role in stabilizing lamina-associated domain (LAD) association with the nuclear lamina, especially during chromatin stress.
• CTCF is essential for anchoring shorter, facultative LADs to the nuclear envelope, highlighting its importance in genome organization under duress.