Active learning of enhancer and silencer regulatory grammar in a developing neural tissue
RZ Friedman, A Ramu, S Lichtarge, Y Wu, L Tripp… - bioRxiv, 2023 - biorxiv.org
Cis-regulatory elements (CREs) direct gene expression in health and disease, and models
that can accurately predict their activities from DNA sequences are crucial for biomedicine …
that can accurately predict their activities from DNA sequences are crucial for biomedicine …
Enhancer cooperativity can compensate for loss of activity over large genomic distances
HF Thomas, S Feng, M Huber, V Loubiere, D Vanina… - bioRxiv, 2023 - biorxiv.org
Enhancers are short DNA sequences that activate their target promoter from a distance;
however, increasing the genomic distance between the enhancer and the promoter …
however, increasing the genomic distance between the enhancer and the promoter …
Massively Parallel Binding Assay (MPBA) reveals limited transcription factor binding cooperativity, challenging models of specificity
T Jana Lang, S Brodsky, W Manadre, M Vidavski… - bioRxiv, 2024 - biorxiv.org
DNA binding domains (DBDs) within transcription factors (TFs) recognize short sequence
motifs that are highly abundant in genomes. In vivo, TFs bind only a small subset of motif …
motifs that are highly abundant in genomes. In vivo, TFs bind only a small subset of motif …
MYC Binding Near Transcriptional End Sites Regulates Basal Gene Expression, Read-Through Transcription and Intragenic Contacts
H Wang, B Ma, T Stevens, J Knapp, J Lu… - bioRxiv, 2024 - biorxiv.org
The MYC oncoprotein regulates numerous genes involved in cellular processes such as cell
cycle and mitochondrial and ribosomal structure and function. This requires …
cycle and mitochondrial and ribosomal structure and function. This requires …
Association between gene expression plasticity and regulatory network topology
AJR Petit, A Genissel, A Le Rouzic - bioRxiv, 2024 - biorxiv.org
Over the past two decades, numerous studies have been conducted with the aim of
identifying the the structures within regulatory networks responsible for gene expression …
identifying the the structures within regulatory networks responsible for gene expression …
A computational approach for deciphering the interactions between proximal and distal regulators in B cell differentiation
SJ Park, K Nakai - bioRxiv, 2023 - biorxiv.org
Delineating the intricate interplay between promoter-proximal and-distal regulators is crucial
for understanding the function of transcriptional mediator complexes implicated in the …
for understanding the function of transcriptional mediator complexes implicated in the …
Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L
M Barsoum, R Sayadi-Boroujeni, AT Stenzel… - bioRxiv, 2023 - biorxiv.org
The trithorax protein ASH2L is essential for organismal and tissue development. As a
subunit of COMPASS/KMT2 complexes, ASH2L is necessary for methylation of histone H3 …
subunit of COMPASS/KMT2 complexes, ASH2L is necessary for methylation of histone H3 …
A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression
R Maritato, A Medugno, E D'Andretta, G De Riso… - bioRxiv, 2023 - biorxiv.org
The binding affinity of transcription factors (TFs) for their cognate DNA sequences controls
gene expression. DNA determines the recruitment and positioning of TFs; whether it plays …
gene expression. DNA determines the recruitment and positioning of TFs; whether it plays …
Sedentary behavior may accelerate aging through impact on epigenome and transcriptome: lessons from muscle inactivation in Drosophila larvae
Aim: The biological mechanisms linking sedentary lifestyles and metabolic derangements
are incompletely understood. Our animal model mimics sedentary behavior during early life …
are incompletely understood. Our animal model mimics sedentary behavior during early life …
Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development
The precisely orchestrated differentiation of chondrocytes during skeleton development is a
critical determinant of human height and body shape and disruptions of this process can …
critical determinant of human height and body shape and disruptions of this process can …