Transcription factor binding site orientation and order are major drivers of gene regulatory activity

I Georgakopoulos-Soares, C Deng, V Agarwal… - Nature …, 2023 - nature.com
The gene regulatory code and grammar remain largely unknown, precluding our ability to
link phenotype to genotype in regulatory sequences. Here, using a massively parallel …

Alternative splicing modulation by G-quadruplexes

I Georgakopoulos-Soares, GE Parada… - Nature …, 2022 - nature.com
Alternative splicing is central to metazoan gene regulation, but the regulatory mechanisms
are incompletely understood. Here, we show that G-quadruplex (G4) motifs are enriched~ 3 …

Tandem repeats ubiquitously flank and contribute to translation initiation sites

AMA Maddi, K Kavousi, M Arabfard, H Ohadi… - BMC Genomic Data, 2022 - Springer
Background While the evolutionary divergence of cis-regulatory sequences impacts
translation initiation sites (TISs), the implication of tandem repeats (TRs) in TIS selection …

[HTML][HTML] Strand asymmetries across genomic processes

C Moeckel, A Zaravinos… - Computational and …, 2023 - Elsevier
Across biological systems, a number of genomic processes, including transcription,
replication, DNA repair, and transcription factor binding, display intrinsic directionalities …

Surveying mutation density patterns around specific genomic features

H Yu, S Ness, CI Li, Y Bai, P Mao, Y Guo - Genome research, 2022 - genome.cshlp.org
Mutation density patterns reveal unique biological properties of specific genomic regions
and shed light on the mechanisms of carcinogenesis. Although previous studies reported …

[PDF][PDF] Tandem repeats ubiquitously ank and select translation initiation sites.

A Maddi, K Kavousi, M Arabfard, H Ohadi, M Ohadi - 2021 - scholar.archive.org
Findings in yeast and human suggest that evolutionary divergence in cis-regulatory
sequences impact translation initiation sites (TISs). Here we employed the TIS homology …