Sarah J. Hainer

This study benchmarks CUT&RUN peak callers using motif enrichment, finding that MACS2 outperforms SEACR in most scenarios with optimal preprocessing.

This study shows that FACT depletion in stem cells causes a sequence of chromatin disruptions leading to transcriptional collapse.

This study investigates the roles of esBAF and INO80C in shaping 3D genome organization in mouse embryonic stem cells, finding they influence subcompartment identity and enhancer-promoter interactions.

The paper shows that the PBAF chromatin remodeling complex regulates metal homeostasis in myoblasts via Mtf1, with metal supplementation compensating for some complex deficiencies.

The paper investigates how nucleosome remodelers affect transcription at cis-regulatory elements in murine ES cells, identifying novel roles and mechanisms of action for different remodelers.

This study identifies FBXO24 as the E3 ligase regulating FoxP1 ubiquitination and stability, revealing bidirectional regulation between the ligase and its substrate.

The paper identifies a silencer element lost in ADLD patients that specifically targets oligodendrocyte overexpression of LMNB1, linking it to disease pathogenesis.

This study identifies mCrip2 as a copper-responsive regulator of skeletal muscle differentiation through functional and biochemical analyses in murine myoblasts.

The paper develops methods to model transcription factor binding in modified DNA by expanding the DNA alphabet and adapting existing tools to handle custom alphabets, identifying modification-sensitive motifs and validating them with experimental data.

This study shows FACT regulates pluripotency in murine embryonic stem cells by controlling nucleosome positioning and gene expression of pluripotency factors.

The paper develops a method to profile TF-DNA interactions in single cells and embryos, showing NANOG's greater reliance on BRG1 in vivo.