Reposted by Takaku LabTeif lab @teiflab.bsky.social · 23/09/2026Zeng et al, 2026. Transcription factors read a second regulatory code in chromatin www.biorxiv.org/content/10.6... "our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture" 1278
Reposted by Takaku LabEpigenome Technologies @epigenometech.bsky.social · 19/05/2026Epigenetics 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.comgo.nature.comWidespread DNA off-targeting confounds RNA chromatin occupancy studies - Nature BiotechnologyMany long noncoding RNA–DNA binding peaks detected using common assays arise from technical artifacts. 022
Takaku Lab @takakulab.bsky.social · 07/05/2026Our 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... 111
Reposted by Takaku LabHarmit Singh Malik @harmitmalik.bsky.social · 03/03/2026My 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...careers-fhcrc.icims.comFred Hutchinson Cancer CenterFred Hutch is dedicated to the elimination of cancer and related diseases as causes of human suffering and death. 13221
Reposted by Takaku LabSarah Hainer @hainerlab.bsky.social · 27/02/2026Incredibly 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...biorxiv.org 14926
Reposted by Takaku Lab@PhysGenCenter @physgencenter.bsky.social · 13/02/2026Friday 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 043
Reposted by Takaku LabArchana Dhasarathy @adhasarathy.bsky.social · 22/01/2026Thank 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! 021
Takaku Lab @takakulab.bsky.social · 13/11/2025Our first cell-free DNA paper is now published! Thank you to all co-authors and collaborators for their contributions. 131
Reposted by Takaku LabDaniel Lipka @dblipka.bsky.social · 25/08/2025+++ 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/... 083
Reposted by Takaku LabEvgeny Kvon @evgenykvon.bsky.social · 23/06/2025How 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/ 310539
Takaku Lab @takakulab.bsky.social · 16/06/2025Structural basis of the hepatitis B virus X protein in complex with DDB1 | PNAS www.pnas.org/doi/10.1073/...pnas.orgStructural basis of the hepatitis B virus X protein in complex with DDB1 | PNASA cure for chronic hepatitis B requires eliminating or permanently silencing covalently closed circular DNA (cccDNA). A pivotal target of this appr... 010
Takaku Lab @takakulab.bsky.social · 16/06/2025RNA transcripts regulate G-quadruplex landscapes through G-loop formation | Science www.science.org/doi/10.1126/...science.orgRNA transcripts regulate G-quadruplex landscapes through G-loop formationG-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... 000
Reposted by Takaku LabJackson Hoffman @jxhoffman.bsky.social · 10/06/2025Congrats 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/...doi.orgPioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodelingAbstract. Pioneer transcription factors (PTFs) bind to inaccessible chromatin and recruit collaborating transcription factors to promote chromatin accessib 0153
Reposted by Takaku LabBroad Institute @broadinstitute.org · 29/05/2025A 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 0236
Takaku Lab @takakulab.bsky.social · 24/03/2025Our 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...researchsquare.comExploring Mechanism of Action of Abemaciclib in Breast Cancer Through Circulating Chromatin FragmentCell free DNA (cfDNA) analysis has a large potential for cancer patient diagnosis. Given the evidence that cfDNA partially preserves chromatin architecture of tumor cells, it potentially allows the de... 032
Reposted by Takaku LabWataru Kobayashi @wkobayashi.bsky.social · 20/02/2025🚀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...biorxiv.org 31810
Reposted by Takaku LabSusanne Ahmari @ahmarilab.bsky.social · 14/02/2025🚨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 🙏🏼wellcomeleap.orgCARE Program Details | Wellcome Leap: Unconventional Projects. Funded at Scale.NEW $50M Program in Women's Health care Cutting Alzheimer's Risk through EndocrinologyWe are pleased to announce the selected performers.Sabine Vollstädt-Klein, Central Institute of Mental Health ... 17989360
Takaku Lab @takakulab.bsky.social · 14/01/2025Excited 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...researchsquare.comATAC-seq Guided Interpretable Machine Learning Reveals Cancer-Specific Chromatin Features in Cell-free DNACell-free DNAs (cfDNAs) are DNA fragments found in blood. In healthy individuals, cfDNAs are primarily derived from immune cells, while in cancer patients, a significant fraction of cfDNAs originates ... 031