Steven Henikoff

The paper identifies elevated polyadenylated histone gene transcription in human cancers, showing it is prevalent across diverse tumor types and linked to RNAPII stabilization.

N3-kethoxal labeling of single-stranded DNA within CUT&Tag maps Pol II transcription bubbles; bubble density tracks nascent transcription, shifts with transcription inhibitors and TFIIS loss, and peaks at histone genes.

FFPE-CUTAC is a new assay for analyzing FFPE tissues that provides regulatory and copy-number profiles, showing robustness over time and compatibility with RNA-seq.

The paper identifies a co-dependency between CDK12 and the BAF chromatin-remodeling complex in TNBC, showing that their co-inhibition synergistically reduces cancer cell viability.

This study identifies aclarubicin's mechanism of action by showing it disrupts RNA polymerase II progression at replication-coupled histone genes, leading to chromatin damage.

The paper tracks H3K27 methylation dynamics in human cells using CUT&Tag, showing that tri-methylation is maintained stepwise after DNA replication and di-methylation occurs at inactive genes post-replication.

The paper identifies superabundant microRNAs transcribed from human rDNA spacer promoters and shows their independent export and potential as cancer biomarkers.

The paper describes a summer research program where students learned chromatin profiling using FFPE-CUTAC, focusing on practical lab techniques and bioinformatics analysis.

The paper identifies histone H4 as a repressor of histone gene transcription during G2 phase in germline cells, showing conserved repression across Drosophila and human cells.

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.

This study develops Nascent CUT&Tag to measure transcription factor binding on nascent chromatin and finds that GAF recovers faster than PHO in Drosophila cells, with differences in motif length and functional associations.

The paper introduces CUT&TIME, a method to map historical chromatin accessibility in single cells during neurogenesis, revealing early changes in promoter accessibility linked to cell-fate commitment in retinal ganglion cells.

The paper shows that total whole-arm chromosome losses predict cancer outcomes across types, suggesting centromere breaks drive aneuploidy rather than mitotic errors.

The paper identifies RNA Polymerase II hypertranscription at histone genes in cancer FFPE samples, linking it to tumor progression and aneuploidy.

This study shows KMT2A oncoproteins drive lineage-switching and epigenetic resistance in leukemia by dynamically binding chromatin and persisting as ENL-marked lesions despite therapy.

The paper shows centromeric arrays can expand and contract in somatic cell divisions, with expansion favored, and identifies RAD52 and PIF1 as required for array changes via break-induced replication.

The paper profiles chromatin features and gene expression in Drosophila male germline to show that sex chromosome inactivation does not occur, and identifies unique epigenetic marks on the Y chromosome.

This study shows aclarubicin increases RNA polymerase II elongation and alters chromatin accessibility and DNA structures in Drosophila cells.

The paper investigates how CTCF-mediated chromatin insulation and structure regulate escape from X chromosome inactivation in mouse cells, showing that CTCF binding and domain organization are critical for maintaining XCI.

The paper investigates how RNA Polymerase II, BAF remodeler, and transcription factors interact to influence nucleosome eviction and chromatin accessibility in mouse embryonic stem cells.

The paper shows boundary-associated RNAs enhance TAD insulation by promoting CTCF clustering at TAD boundaries.

This study introduces MulTI-Tag, a method to profile multiple chromatin features in single cells, revealing coordinated regulatory patterns and novel histone mark associations.

The paper introduces RT&Tag, a method to profile chromatin-associated RNAs by antibody-targeted tagmentation, demonstrating its ability to capture noncoding RNAs and m6A-modified mRNAs in Drosophila cells.

The paper describes a modified CUT&Tag protocol that profiles both active and repressive regulatory elements in single cells using computational signal deconvolution.

This paper introduces TIP-seq, a high-throughput single-cell method for mapping DNA binding sites, achieving higher coverage and signal-to-noise than existing methods.

The paper develops an automated CUT&Tag method to profile chromatin occupancy of KMT2A fusion proteins in leukemia samples, revealing epigenomic heterogeneity and therapeutic sensitivity.

This study shows that the H3.3K27M oncohistone blocks eye-to-wing reprogramming in Drosophila by reducing H3K27me3 domains and synergizes with mis-expressed transcription factors to cause tissue overgrowth.

The paper reanalyzes ChEC-seq data to show that short-duration experiments produce specific transcription factor binding maps in budding yeast.

This study shows that Firre RNA has trans-acting effects on the inactive X chromosome, affecting histone modifications, PRC2 complex components, and chromatin structure.

This study shows that H3.1 and H3.3 K27M oncohistones affect chromatin landscapes differently in DMG cells, with H3.1K27M leading to loss of H3K27 trimethylation.