Latest updates for Chromatin Accessibility

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Recent items include:

  • Asymmetric chromatin accessibility underlies anterior-posterior axis specification in moth fly embryos
  • Improved spike-in normalization reveals how active histone modifications relate to transcription
  • Systematic multivariate analysis of chromatin complex dependencies reveals Set1C/COMPASS as a melanoma-enriched epigenet

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journals.plos.org /1 month ago

Asymmetric chromatin accessibility underlies anterior-posterior axis specification in moth fly embryos

by Ezra E. Amiri, Muzi Li, Ayse Tenger-Trolander, Maxwell Devine, Alexander T. Julian, Koray Kasan, Sheri A. Sanders, Shelby A. Blythe, Urs Schmidt-Ott Establishing the anterior-p...

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bioengineer.org /2 weeks ago

Improved spike-in normalization reveals how active histone modifications relate to transcription

Chromatin, the molecular packaging system that compacts DNA inside the nucleus, is not merely a passive storage device. By loosening or tightening access to genetic material, it he...

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journals.plos.org /1 week ago

Systematic multivariate analysis of chromatin complex dependencies reveals Set1C/COMPASS as a melanoma-enriched epigenet...

by Luisa Quesada Camacho, Mohammad Fallahi-Sichani Epigenetic dysregulation is a common feature of cancer. It creates vulnerabilities arising from an increased reliance on chromat...

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phys.org /2 weeks ago

DNA's physical properties may shape which mutations evolution preserves

Nearly every cell in the human body contains essentially the same genetic information, yet different cells activate different genes. For regulatory proteins to reach these genes, D...

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bioengineer.org /4 weeks ago

OneCell CUT&Tag Maps Chromatin, Transcripts and Surface Markers, Revealing Epigenomic Reprogramming

A new single-cell technology is giving researchers an unusually complete view of how individual cells establish and change their identities. Called OneCell CUT&Tag, the method...

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journals.plos.org /1 month ago

Wiz regulates clustered protocadherin genes by restricting CTCF/cohesin loop extrusion in a genomic-distance biased mann...

by Tianjie Li, Jingwei Li, Leyang Wang, Haiyan Huang, Qiang Wu Zinc finger proteins (ZFPs or ZNFs) constitute the largest family of transcription factors in mammals; however, thei...

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journals.plos.org /1 month ago

Deciphering chromatin architecture and dynamics in <i>Plasmodium falciparum</i> using the nucDetective pipel...

by Simon Holzinger, Leo Schmutterer, Victoria Marie Rothe, Maria Theresia Watzlowik, Uwe Schwartz, Gernot Längst High-resolution analysis of cellular chromatin structure is crucia...

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genengnews.com /1 month ago

Single-Cell Atlas Simultaneously Maps 3D Genome Architecture and DNA Methylation

Atlases like this one can provide the labeled, cell-type-resolved training data that artificial intelligence models need to make accurate predictions—a bottleneck that has historic...

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rna-seqblog.com /1 month ago

Learning the grammar of gene regulation

RNA sequencing data helped power an AI model that predicts gene regulation across cell types, improving the interpretation of genomic activity and supporting future precision medic...

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journals.plos.org /1 month ago

The G-force in the genome: Unknowns on the functional flairs of DNA G-quadruplexes

by Irene Gallina, Sara N. Richter Alternative DNA secondary structures known as G-quadruplexes (G4s) form across all kingdoms of life, regulating transcription, telomere stability...

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journals.plos.org /2 weeks ago

Tcf15 promotes an open nucleolar chromatin state to safeguard ribosome biogenesis and genome stability in mouse embryoni...

by Yu-ping Dong, Yi-Min Chen, Min Tang, Hu Zhou, Lin Wang, Ping Zheng Embryonic stem cells (ESCs) exhibit a hyperactive chromatin state at ribosomal RNA (rRNA) genes, which not on...

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genengnews.com /1 month ago

Genome-Scale CRISPRi Atlas Maps Gene Function Across Human iPSCs

A genome-scale CRISPRi atlas maps transcriptional consequences for 11,692 gene perturbations across more than 2.5 million human iPSCs. The resource reveals regulators of metabolism...

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genengnews.com /1 month ago

Spatiotemporal Multiomics Charts Cellular Dynamics of Liver Metastasis

The team integrated high-resolution spatial transcriptomics, single-cell RNA sequencing, and chromatin-accessibility profiling across nine sequential stages of lung colonization in...

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bioengineer.org /2 weeks ago

How Cancer-Causing 3D Chromatin Remodeling Begins and Shapes Disease

Cancer does not merely rewrite the genetic letters of the genome; it can also reorganize the vast three-dimensional structure in which those letters are stored. A new review by Fra...

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journals.plos.org /1 month ago

Motif-cluster: Motif driven prioritization of transcription factor binding clusters

by Mengyuan Zhou, Qiuming Yao Genome-wide analyses of transcription factor (TF) motif binding sites have largely emphasized individual high-affinity sites, while overlooking the r...

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rna-seqblog.com /3 weeks ago

Novel electromagnetically tunable gene switch enables precise control of gene expression

Single-cell RNA sequencing identified an electromagnetic field-responsive gene, enabling researchers to develop a reversible switch for precise, non-invasive control of gene expres...

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scitechdaily.com /1 month ago

Unzipping the Code of Life: Scientists Pinpoint Where DNA First Opens

Researchers mapped where DNA first opens and how a helicase gate may release one strand as genome copying begins. Before a cell can divide, it must open its tightly wound DNA and b...

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nanowerk.com /1 month ago

New AI-based tool allows to predict activity of DNA sequences

A context-aware AI tool predicts how genomic DNA behaves across different cell types, supporting more accurate virtual cell models for research and medicine.

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rna-seqblog.com /1 month ago

DeepDETAILS – high-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequen...

DeepDETAILS combines artificial intelligence with RNA sequencing and chromatin data to reconstruct cell-specific gene regulation from bulk tissue sequencing experiments...

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journals.plos.org /1 month ago

Accurate <i>de novo</i> transcription unit annotation from run-on and sequencing data

by Paul R. Munn, Jay Chia, Charles G. Danko Functional element annotations are critical tools used to provide insight into the molecular processes governing cell development, diff...

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blog.google /1 day ago

AlphaGenome Atlas: a high-resolution map of human DNA

We’re introducing AlphaGenome Atlas, a database predicting the effects of every possible single nucleotide variant in the human genome.

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journals.plos.org /1 month ago

Quantitative modelling of P-TEFb mediated CTD phosphorylation identifies local cooperativity

by Aaron Callenbach, Domagoj Dorešić, Robert Düster, Vanessa Nakonecnij, Erika Dudkin, Matthias Geyer, Jan Hasenauer Fine-tuned regulation of RNA polymerase II (Pol II) activity i...

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journals.plos.org /1 week ago

Pervasive context-dependent effects in the genetic architecture of complex and quantitative traits revealed by a powerfu...

by Gareth A. Cromie, Russell S. Lo, Lauren Ames, Trey S. Morgan, Katherine Owens, Anne E. Clark, Martin S. Timour, Julee Ashmead, Michelle Tang, J. Nathan Kutz, Joshua M. Akey, Aim...

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rna-seqblog.com /1 week ago

ARCADIA combines RNA sequencing and spatial proteomics to reveal how tissue location shapes cell behavior

ARCADIA integrates single-cell RNA sequencing with spatial proteomics to reveal how tissue neighborhoods influence B-cell maturation, T-cell activation, and other transcriptional p...

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