Epigenetics Update - Widespread DNA off-targeting confounds RNA chromatin occupancy studies go.nature.com/3PmKDVa Pieter Mestdagh (Ghent University) and igorulitsky.bsky.social (Weizmann Institute of Science) in natbiotech.nature.com #Epigenetics #Chromatin #OffTarget --- epigenometech.com

Widespread DNA off-targeting confounds RNA chromatin occupancy studies - Nature Biotechnology

Many long noncoding RNA–DNA binding peaks detected using common assays arise from technical artifacts.

go.nature.com

Our new paper is out in Communications Medicine! By analyzing circulating chromatin fragments (cfDNA) from patients with metastatic breast cancer, we captured treatment-associated fragmentomics changes after CDK4/6 inhibitor therapy. Grateful to all collaborators! www.nature.com/articles/s43...

My awesome colleague, @yarimura.bsky.social, is recruiting a postdoc to start at the end of 2026 or early 2027! His lab uses cryo-EM to uncover structural basis of key chromatin events using native complexes isolated from human cells or Xenopus egg extracts! careers-fhcrc.icims.com/jobs/30706/p...

Fred Hutchinson Cancer Center

Fred Hutch is dedicated to the elimination of cancer and related diseases as causes of human suffering and death.

careers-fhcrc.icims.com

Incredibly proud to share our new preprint, lead by the Incomparable Rithika Sankar. Here we temporally dissect the role of FACT in mES cells, finding that FACT loss drives progressive deterioration of chromatin architecture, leading to transcriptional collapse. www.biorxiv.org/content/10.6...

Friday Feb. 27 at 12pm CT, Prof. Steve Henikoff presents the Monthly Seminar on Physical Genomics: "Histone Overexpression In Cancer" live on Zoom! Registration is free at tinyurl.com/2rw8n7bt #northwestern #cancer #genomics #research #chromatin #dna #science #biology #cpge #fredhutch #research

Thank you so much for the great talk and wonderful science conversations! @takakulab.bsky.social and our students and other faculty really appreciated your sharing your science with us!

Teif lab@teiflab.bsky.social · 8mo ago

Today we had very nice interactions in the University of North Dakota (remotely)! Thank you very much @adhasarathy.bsky.social, Motoki Takaku & Co for the invitation to give this talk and hosting the visit!

Our first cell-free DNA paper is now published! Thank you to all co-authors and collaborators for their contributions.

Sakuntha D. Gunarathna@sakuntha.bsky.social · 10mo ago

Officially published in Communications Biology! In this study, we developed an open chromatin-guided, interpretable machine learning pipeline to uncover cancer-specific nucleosomal fragment patterns directly from cell-free DNA. 📄 Published article: doi.org/10.1038/s420...

+++ Postdoc Opportunity +++ My lab is looking for researchers interested in combining cutting edge #genomics, #epigenetics and #AI for precision oncology in pediatric #leukemia. www.dkfz.de/fileadmin/us... Applications via the #DKFZ postdoc program: www.dkfz.de/en/karriere/...

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

Structural basis of the hepatitis B virus X protein in complex with DDB1 | PNAS www.pnas.org/doi/10.1073/...

Structural basis of the hepatitis B virus X protein in complex with DDB1 | PNAS

A cure for chronic hepatitis B requires eliminating or permanently silencing covalently closed circular DNA (cccDNA). A pivotal target of this appr...

pnas.org

RNA transcripts regulate G-quadruplex landscapes through G-loop formation | Science www.science.org/doi/10.1126/...

RNA transcripts regulate G-quadruplex landscapes through G-loop formation

G-quadruplexes (G4s) are prevalent DNA structures that regulate transcription but also threaten genome stability. How G4 dynamics are controlled remains poorly understood. Here, we report that RNA tra...

science.org

Congrats on the new paper to Krystal who "doesn't do social media" but does do a ton of ATAC and Cut&Run to show how GATA3 pioneers enhancers with BRG1 and sometimes AP-1! #NIEHS #NAR doi.org/10.1093/nar/...

Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling

Abstract. Pioneer transcription factors (PTFs) bind to inaccessible chromatin and recruit collaborating transcription factors to promote chromatin accessib

doi.org

A new combination technique enables DNA sequencing and high-resolution imaging in intact cells — offering new insights into progeria and aging. broad.io/expansion-in-situ @jbuenrostro.bsky.social

Our second cell-free DNA manuscript is here! In collaboration with Dr. Takada’s group, we explore how abemaciclib treatment response in metastatic breast cancer can be monitored via circulating chromatin fragments: www.researchsquare.com/article/rs-5...

🚀Excited to share preprint as my last work in the Tachibana lab! Our study shows how the pioneer factor NR5A2 ensures robust gene activation through feed-forward regulatory loops with lineage-determining factors. A quick summary follows (1/n) www.biorxiv.org/content/10.1...

🚨Amidst all the uncertainty at NIH Welcome Leap just launched an important new $50M program in Women’s Health👩🏻‍🔬🧠 CARE focuses on the link between Alzheimer’s and perimenopausal hormonal changes wellcomeleap.org/care/ Note: full indirects! Please share widely to support women’s health 🙏🏼

Excited to share our first preprint on cell-free DNA! Led by our talented grad student Sakuntha, we have developed a machine learning pipeline guided by ATAC-seq to identify unique nucleosomal fragment patterns in cancer patients. www.researchsquare.com/article/rs-5...