Long range regulation of transcription scales with genomic distance in a gene specific manner

CL Jensen, LF Chen, T Swigut, OJ Crocker, D Yao… - bioRxiv, 2024 - biorxiv.org
While critical for tuning the timing and level of transcription, enhancer communication with
distal promoters is not well understood. Here we bypass the need for sequence-specific …

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

S Naqvi, S Kim, S Tabatabaee, A Pampari, A Kundaje… - bioRxiv, 2024 - biorxiv.org
Deep learning approaches have made significant advances in predicting cell type-specific
chromatin patterns from the identity and arrangement of transcription factor (TF) binding …

Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation

D Vucicevic, CW Hsu, LS Lopez Zepeda, M Burkert… - bioRxiv, 2024 - biorxiv.org
Transcriptional enhancers are non-coding DNA elements that regulate gene transcription in
a temporal and tissue-specific manner. Despite advances in computational and …

Mechanistic dissection of the CHD4 enhancers reveals cooperative functions among the homotypic ZNF410 clustered motifs

S Xu, R Ren, C Peng, H Lu, LC Ly, M Crossley, B Xu… - bioRxiv, 2024 - biorxiv.org
Transcription factors often regulate numerous target genes. However, ZNF410 controls only
a single gene, CHD4, in human erythroid cells by its highly restricted chromatin occupancy …

Dissecting the dynamics of coordinated active transcriptional repression in a multicellular organism

V Pimmett, M Douaihy, L Maillard, A Trullo, J Dufourt… - bioRxiv, 2024 - biorxiv.org
The ability to refine transcriptional levels via active repression in an euchromatic context
represents a critical regulatory process during development. While the molecular players of …

Integrated functional genomic analysis identifies the regulatory variants underlying a major QTL for disease resistance in European sea bass

R Mukiibi, S Ferraresso, R Franch, L Peruzza… - bioRxiv, 2024 - biorxiv.org
Background: Viral nervous necrosis (VNN) is a viral disease threatening the sustainability of
global aquaculture, and affecting over 50 of farmed and ecologically important species. A …

[HTML][HTML] Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration

K Wu, N Dhillon, A Bajor, S Abrahamson… - bioRxiv, 2023 - ncbi.nlm.nih.gov
The interplay between nucleosomes and transcription factors leads to programs of gene
expression. Transcriptional silencing involves the generation of a chromatin state that …

Cooperativity and additivity in plant enhancers

T Jores, J Tonnies, NA Mueth, A Romanowski, S Fields… - bioRxiv, 2023 - biorxiv.org
Enhancers are cis-regulatory elements that shape gene expression in response to
numerous developmental and environmental cues. In animals, several models have been …

A Bag-Of-Motif Model Captures Cell States at Distal Regulatory Sequences

P Cornejo, X Zhang, L Louis, Y Yang, Z Li… - bioRxiv, 2024 - biorxiv.org
Deciphering the intricate regulatory code governing cell-type-specific gene expression is a
fundamental goal in genetics. Current methods struggle to capture the complex interplay …

A novel hybrid promoter capable of continuously producing proteins in high yield

H Lee, ES Song, YH Lee, JY Park, MU Kuk… - Biochemical and …, 2023 - Elsevier
The establishment of cell lines with a high protein production is the most crucial objective in
the field of biopharmaceuticals. To this end, efforts have been made to increase transgene …