The paper shows that DNA methylation in bivalent promoters can activate genes by displacing repressive marks, and this mechanism is relevant in cancer.

bioRxiv · Feb 7, 2025 · PreprintGenomics

Integration of CTCF Loops, Methylome, and Transcriptome in Differentiating LUHMES as a Model for Imprinting Dynamics of the 15q11-q13 Locus in Human Neurons

Orangel J. Gutierrez Fugón, Osman Sharifi, Nicholas G. Heath, Daniela C. Soto, J. Antonio Gomez, Dag H. Yasui, Aron Judd P. Mendiola, Henriette O’Geen, Ulrika Beitnere, Markéta Tomková, Viktoria Haghani, Greg Dillon, David Jay Segal, Janine M. LaSalle

The paper integrates CTCF loops, methylome, and transcriptome data from LUHMES neurons to study imprinting dynamics at the 15q11-q13 locus during differentiation.

Human Molecular Genetics · Jul 24, 2024Peer-reviewedGenetics

Diverse molecular mechanisms contribute to differential expression of human duplicated genes

Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O’Geen, Megan Y. Dennis

The paper investigates differential expression of human duplicated genes and finds cis-regulatory divergence contributes to novel expression patterns in recent gene duplicates.

Molecular Biology and Evolution · Apr 28, 2021Peer-reviewedGenomics

Imprinting effects of UBE3A loss on synaptic gene networks and Wnt signaling pathways

S. Jesse Lopez, Benjamin I. Laufer, Ulrika Beitnere, Elizabeth L. Berg, Jill L. Silverman, Henriette O’Geen, David Jay Segal, Janine M. LaSalle

This paper investigates the molecular impacts of UBE3A loss in a novel rat model of Angelman syndrome using systems biology approaches, revealing epigenetic network interactions between maternal and paternal transcripts.

Human Molecular Genetics · Oct 8, 2019Peer-reviewedGenomics