Kami Ahmad

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.

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 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.

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 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 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 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 introduces nanoCUT&RUN, a modified CUT&RUN technique for mapping chromatin protein binding sites in Drosophila, showing its effectiveness for TRL, HipHop, and HOAP proteins.

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

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 characterizes TF cooperativity at active enhancers in Drosophila using nuclease footprinting and chromatin profiling, finding that cooperativity is common and facilitates enhancer function.

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.

This paper develops scCUT&Tag to profile H3K27me3 in single cells, distinguishing cell types in blood and identifying PcG activity changes in brain tumors before and after treatment.

The paper introduces a modified CUT&Tag method that produces chromatin accessibility maps comparable to ATAC-seq by adjusting tagmentation conditions for H3K4me2 or H3K4me3.

The paper shows that two PREs near the vestigial gene have distinct roles in gene activation and chromatin modification, challenging the idea that PREs solely repress gene expression.

The paper introduces CUT&Tag, a method for high-resolution epigenomic profiling of small samples and single cells with low background and efficient library preparation.

The paper introduces an automated CUT&RUN platform to profile chromatin modifications in human cell lines and tumor samples, revealing cell-type specific gene regulatory programs.