Mitchell Guttman

This paper introduces LagTag, a method to recover both earlier and endpoint chromatin states in mammalian cells, and applies it to study dynamic chromatin transitions during stem cell differentiation.

This study shows that LBR nucleoplasmic domains regulate X-chromosome solubility and nuclear organization during neural differentiation in mouse cells.

The paper shows that MALAT1 long noncoding RNA forms condensates with splicing factors to regulate hypoxia-induced alternative splicing near nuclear speckles.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

RAP-MS 2.0 improves specificity and throughput for identifying RNA-binding proteins by reducing background and enabling reuse of lysate for multiple RNA captures.

SPIDR is a high-throughput method for mapping RNA-protein interactions that identifies 4EBP1's role in selectively repressing mRNA translation under mTOR inhibition.

This study uses high-resolution spatial multi-omics to analyze subnuclear compartments in single cells, revealing cell-type specific chromatin structures and their genomic associations.

ChIP-DIP enables simultaneous mapping of hundreds of regulatory proteins to DNA, revealing diverse regulatory elements and their functional activity.

The paper identifies that ignoring RNA quantity in analysis leads to inflated background signals and misleading conclusions about PRC2 and GFP RNA binding.

The paper shows that gene proximity to nuclear speckles increases spliceosome binding and co-transcriptional splicing efficiency, highlighting the role of 3D genome organization in mRNA splicing.

The paper develops RD-SPRITE to map RNA-DNA and RNA-RNA interactions in 3D nuclear structures, revealing RNA's role in forming compartments that regulate nuclear functions.

This study shows Xist uses spatial amplification of SHARP to achieve chromosome-wide silencing while maintaining specificity to the X chromosome.

The paper maps chromatin states, DNA loci, and gene expression in single mouse embryonic stem cells using DNA seqFISH+ and immunofluorescence, revealing nuclear zones and subpopulations with distinct chromatin features.

The paper shows that Xist RNA forms a protein condensate with binding proteins to establish the Xi-compartment and maintain gene silencing.

The paper introduces SPRITE, a method for detecting higher-order DNA interactions, and shows that nuclear bodies act as inter-chromosomal hubs shaping 3D genome organization.

The paper outlines the goals and structure of the 4D Nucleome Project, which aims to map the spatial and temporal dynamics of the genome in human and mouse cells.