Position-dependent effects of transcription factor binding

K Minton - Nature Reviews Genetics, 2024 - nature.com
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Q-rich activation domains: flexible 'rulers' for transcription start site selection?

A Bernardini, R Mantovani - Trends in Genetics, 2024 - cell.com
Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter
motifs from quantitative regulators of transcription to important determinants of transcription …

Enhancers associated with unstable RNAs are rare in plants

BR Mcdonald, CL Picard, IM Brabb, MI Savenkova… - Nature Plants, 2024 - nature.com
Unstable transcripts have emerged as markers of active enhancers in vertebrates and
shown to be involved in many cellular processes and medical disorders. However, their …

Dissecting the cis-regulatory syntax of transcription initiation with deep learning

K Cochran, M Yin, A Mantripragada, J Schreiber… - …, 2024 - pmc.ncbi.nlm.nih.gov
Despite extensive characterization of mammalian Pol II transcription, the DNA sequence
determinants of transcription initiation at a third of human promoters and most enhancers …

[HTML][HTML] Chromosome-level genome assembly of Pteroceltis tatarinowii provides new insights into evolution and fiber biosynthesis

Q Qiao, J Wang, J Wang, Y Yan, Z Sun, L Zhang… - Industrial Crops and …, 2025 - Elsevier
Pteroceltis tatarinowii, a unique single-species plant and fibrous tree in China, is the raw
material for making Xuan paper. However, the lack of a complete genome sequence has …

Human stem cell-specific epigenetic signatures control transgene expression

CS Kwak, FE Oflaz, J Qiu, X Wang - Biochimica et Biophysica Acta (BBA) …, 2024 - Elsevier
Human stem cell-derived models have emerged as an important platform to study tissue
differentiation and disease mechanisms. Those models could capitalize on biochemical and …

Efficient small fragment sequencing of human, cattle, and bison miRNA, small RNA, or csRNA-seq libraries using AVITI

AL McDonald, AM Boddicker, MI Savenkova, IM Brabb… - BMC genomics, 2024 - Springer
Abstract Background Next-Generation Sequencing (NGS) catalyzed breakthroughs across
various scientific domains. Illumina's sequencing by synthesis method has long been central …

[HTML][HTML] Should Artificial Intelligence Play a Durable Role in Biomedical Research and Practice?

P Bongrand - International Journal of Molecular Sciences, 2024 - mdpi.com
During the last decade, artificial intelligence (AI) was applied to nearly all domains of human
activity, including scientific research. It is thus warranted to ask whether AI thinking should …

Non-canonical hepatic androgen receptor mediates glucagon sensitivity in female mice through the PGC1α/ERRα/mitochondria axis

J Chen, Y Wu, W Hao, J You, L Wu - Cell Reports, 2025 - cell.com
Glucagon has recently been found to modulate liver fat content, in addition to its role in
regulating gluconeogenesis. However, the precise mechanisms by which glucagon …

Exploring the Potentials and Challenges of Using Large Language Models for the Analysis of Transcriptional Regulation of Long Non-coding RNAs

W Wang, Z Hou, X Liu, X Peng - arXiv preprint arXiv:2411.03522, 2024 - arxiv.org
Research on long non-coding RNAs (lncRNAs) has garnered significant attention due to
their critical roles in gene regulation and disease mechanisms. However, the complexity and …