Kyle N. Klein

A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)

The paper presents a hiPS cell model to study EMTs by comparing 2D and 3D cultures, measuring changes in cell function, markers, organization, and environment.

Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories

The paper analyzes nuclear growth variations in hiPS cell colonies, finding context-dependent and inherited mechanisms shaping growth trajectories.

Enhanced endogenous gene tagging in human induced pluripotent stem cells via AAV6-mediated donor delivery

This paper develops a method to efficiently insert fluorescent tags into genes not expressed in hiPSCs using AAV6 delivery, optimized CRISPR conditions, and ddPCR/ICE to minimize INDELs and isolate tagged clones.

RIF1 regulates replication origin activity and early replication timing in B cells

This study shows RIF1 regulates early replication timing and origin activity in B cells by interacting with MCM proteins, influencing gene replication without major effects on gene expression or genome organization.

Cohesin-mediated loop anchors confine the location of human replication origins

This study shows that cohesin-mediated loops in G1 phase determine the genomic location of replication origins in S phase by anchoring replication initiation zones.

Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication

This study uses Optical Replication Mapping to map human DNA replication initiation sites and finds that replication initiation is stochastic and not confined to specific origins.

Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction

This study identifies RIF1 as a molecular hub that co-regulates nuclear organisation and replication timing through its interaction with PP1, revealing distinct functional requirements for these processes.

Replication timing maintains the global epigenetic state in human cells.

This study shows that replication timing (RT) is essential for maintaining the global epigenetic state and genome compartmentalization in human cells, with RIF1 playing a central role in this process.

Catalytically Enhanced Cas9 through Directed Protein Evolution

This paper describes a directed protein evolution method to enhance the catalytic efficiency of CRISPR-Cas9 variants, showing up to 4-fold improvement in AceCas9 and 2-fold increase in HDR-based gene insertion for SpyCas9.

Identification of cis elements for spatio-temporal control of DNA replication

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping

This study identifies early-firing human replication origins in HeLa cells using Optical Replication Mapping, revealing that initiation occurs across broad zones rather than confined to efficient origins.