Results 61 to 70 of about 800,836 (279)

Synergistic perspectives—How single‐molecule biophysics complement biochemical understanding

FEBS Letters, EarlyView.
In this review, we discuss how ensemble biochemistry and single‐molecule approaches are complementary, outline commonly used single‐molecule techniques, and illustrate their relevance through two representative case studies: chromatin organization by SMC complexes and pathway choice during DNA double‐strand break repair.
Sara De Bragança, Eline L. Jansen, Jorine M. Eeftens   +2 more
wiley   +1 more source

Proteins driving liquid-liquid phase separation and histone modifications cooperatively associate with chromatin looping and transcriptional regulation

Epigenetics & Chromatin
Background Although liquid-liquid phase separation (LLPS) proteins are known to participate in genome organization and transcriptional regulation through the formation of biomolecular condensates, their functional interplay with other regulatory proteins
Xue Ji, Yumin Nie
doaj   +1 more source

Integrating extrusion complex-associated pattern to predict cell type-specific long-range chromatin loops

iScience, 2022
Summary: The chromatin loop plays a critical role in the study of gene expression and disease. Supervised learning-based algorithms to predict the chromatin loops require large priori information to satisfy the model construction, while the prediction ...
Yajing Deng, Li Tang, Xiaolong Zhou, Wenkang Wang, Min Li   +4 more
doaj   +1 more source

From junk to function — How weak selection in eukaryotes builds new parts and drives genomic complexity

FEBS Letters, EarlyView.
How do genomes gain new functional parts? In eukaryotes, which tend to evolve under weak selection, much of the genome is junk. Palazzo and Qiu borrow the logic of Markov chains to show how non‐functional DNA becomes functional through the appearance of intermediate states, which arise due to epistasis, buffering, and biochemical messiness, allowing ...
Alexander F. Palazzo, Yi Qiu
wiley   +1 more source

CellLoop: Identifying single-cell 3D genome chromatin loops

Nature Communications
Single-cell 3D genome technologies provide unprecedented views of chromatin architecture, but the extreme sparsity and noise of contact maps limit robust detection of chromatin loops at the individual cell level. Here we present CellLoop, a computational
Yusen Ye, Yiheng Wang, Shiji Liu, Yuxuan Hu, Liang Yu, Weibing Wang, Shihua Zhang, Hebing Chen, Lin Gao   +8 more
doaj   +1 more source

BET family BRD3 initiates DSB-induced chromatin remodeling with TIP60 to promote R-loop-mediated HR

Cell Reports
Summary: Mechanisms for genome stability in actively transcribed regions are essential for cellular homeostasis; however, these mechanisms are poorly understood. Herein, we identify the bromodomain and extraterminal domain (BET) family BRD3 as the genome
Jianghao Qian, Tomoko Watanabe, Reiko Watanabe, Shin-ichiro Kanno, Akiko Takahashi, Shinji Kohsaka, Yuki Yoshino, Natsuko Chiba, Kozo Tanaka, Takashi Kohno, Akira Yasui, Ayako Ui   +11 more
doaj   +1 more source

TAD cliques predict key features of chromatin organization

BMC Genomics, 2021
Background Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and interactions with the nuclear ...
Tharvesh M. Liyakat Ali, Annaël Brunet, Philippe Collas, Jonas Paulsen   +3 more
doaj   +1 more source

Loop Interrupted: Dysfunctional Chromatin Relations in Neurological Diseases

Frontiers in Genetics, 2021
The majority of genetic variants for psychiatric disorders have been found within non-coding genomic regions. Physical interactions of gene promoters with distant regulatory elements carrying risk alleles may explain how the latter affect gene expression.
Marthe Behrends, Olivia Engmann
doaj   +1 more source

Linking Differential Chromatin Loops to Transcriptional Decisions [PDF]

Molecular Cell, 2008
GATA-1 and GATA-2 control proliferation and differentiation of hematopoietic progenitor cells via transcriptional regulation. In this issue of Molecular Cell, Jing et al. (2008) demonstrate that GATA factor exchange on the Kit locus directs a transcriptional switch by reconfiguring chromatin loops.
Apostolou, Effie, Thanos, Dimitris
openaire   +2 more sources

One Speaker/One Poem: Jeremy Elprin on John Keats

, 2022
Jeremy Elprin (Université de Caen Normandie) will be presenting John Keats's poem "On First Looking into Chapman's Homer". The session will be moderated by Marc Porée You can follow the presentation on YouTube via this link (or via Zoom for the LOOP ...
The LOOP team
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