Mary Ann Allen

Common cis-eQTLs do not explain chromosome 21 expression deviations from the ploidy expectation in Down syndrome

The paper investigates whether common cis-eQTLs explain gene expression deviations from ploidy expectations in Down syndrome using transcriptomic data from the Human Trisome Project and GTEx.

Attenuated estrogen signaling disrupts placentation and drives trophoblast defects in Down syndrome

This study identifies attenuated estrogen signaling and NRIP1 as key factors in trophoblast defects in Down syndrome using patient-derived stem cells.

Improving confidence of differential transcription calls in enhancers

The paper introduces two algorithms, Mu Counts and TFEA-LE, to improve the identification of differentially transcribed regulatory elements by integrating motif information and enhancing precision and recall.

Base Composition Influences the Position andPrecision of RNA Polymerase II Disassociation inBasal and Perturbed Conditions.

The paper identifies two types of Pol II disassociation regions, differing in base composition and sensitivity to cellular perturbations.

LIET Model: Capturing the kinetics of RNA polymerase from loading to termination

The paper introduces the LIET model to analyze RNA polymerase kinetics across transcription stages and applies it to human cell-types and perturbation experiments to detect changes in transcription dynamics.

Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome

This study shows that inhibiting Mediator kinases CDK8/CDK19 suppresses hyperactive IFN signaling in Down syndrome by affecting transcription, splicing, and lipid metabolism.

Histone Deacetylase Inhibitor Largazole Deactivates A Subset of Superenchancers and Causes Mitotic Chromosome Mis-alignment by Suppressing SP1 and BRD4

This study shows largazole suppresses superenhancer accessibility by inhibiting SP1 and BRD4, leading to mitotic chromosome misalignment and cell cycle arrest.

Single nucleus RNA-sequencing reveals transcriptional synchrony across different relationships

The paper uses single nucleus RNA-sequencing to show transcriptional synchrony between prairie voles in social relationships, identifying genes in oligodendrocyte progenitor cells linked to dyadic behavior.

A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networks

TF profiler infers transcription factor activity from PRO-seq and GRO-seq data, identifying three distinct TF classes based on regulatory roles.

Atlas of nascent RNA transcripts reveals enhancer to gene linkages

The paper identifies over 800,000 bidirectional transcription regions in human samples and links them to genes through correlated transcription, enriched for disease SNPs and supported by 3D data.

Cellular zinc status alters chromatin accessibility and binding of transcription factor TP53 to genomic sites

The paper shows that changes in labile zinc levels affect chromatin accessibility and TP53 binding to DNA.

Transcription dosage compensation does not occur in Down syndrome

The paper shows that transcriptional dosage compensation is absent in Down syndrome using real and simulated data, and highlights issues with standard analysis methods.

Characterizing Primary transcriptional responses to short term heat shock in paired fraternal lymphoblastoid lines with and without Down syndrome.

The paper investigates the heat shock response in lymphoblastoid cell lines with and without trisomy 21, finding a more robust response in trisomy 21 cells.

Myonuclear maturation dynamics in aged and adult regenerating mouse skeletal muscle

The paper investigates myonuclear maturation dynamics in aged and adult regenerating mouse skeletal muscle, finding that transcriptional heterogeneity arises during maturation and is altered in aged muscle.

Heat Shock in C. elegans Induces Downstream of Gene Transcription and Accumulation of Double-Stranded RNA

The paper shows heat shock in C. elegans increases antisense transcripts and downstream of gene transcripts, which accumulate as dsRNA foci overlapping with HSF-1 granules.

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

The paper uses GRO-seq to show glucocorticoids rapidly repress transcription without local GR occupancy and induce anti-inflammatory effects through GR-NF-kB cooperation.

Detecting differential transcription factor activity from ATAC-seq data

The paper demonstrates a method to detect differential transcription factor activity using ATAC-seq data by analyzing TF recognition motifs relative to open chromatin regions.