The causes and consequences of genetic interactions (epistasis)
J Domingo, P Baeza-Centurion… - Annual review of …, 2019 - annualreviews.org
The same mutation can have different effects in different individuals. One important reason
for this is that the outcome of a mutation can depend on the genetic context in which it …
for this is that the outcome of a mutation can depend on the genetic context in which it …
Molecular dynamics simulations of DNA–DNA and DNA–protein interactions
Highlights•Standard force fields prescribe overly attractive DNA-DNA and DNA-protein
interactions.•Recently improved force fields enable simulations that reproduce and predict …
interactions.•Recently improved force fields enable simulations that reproduce and predict …
Short tandem repeats bind transcription factors to tune eukaryotic gene expression
CA Horton, AM Alexandari, MGB Hayes, E Marklund… - Science, 2023 - science.org
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter
gene expression, yet how they regulate transcription remains unknown. We found that STRs …
gene expression, yet how they regulate transcription remains unknown. We found that STRs …
Systematic analysis of binding of transcription factors to noncoding variants
Many sequence variants have been linked to complex human traits and diseases, but
deciphering their biological functions remains challenging, as most of them reside in …
deciphering their biological functions remains challenging, as most of them reside in …
[HTML][HTML] The prognostic potential of CDX2 in colorectal cancer: Harmonizing biology and clinical practice
J Badia-Ramentol, F Gimeno-Valiente… - Cancer Treatment …, 2023 - Elsevier
Adjuvant chemotherapy following surgical intervention remains the primary treatment option
for patients with localized colorectal cancer (CRC). However, a significant proportion of …
for patients with localized colorectal cancer (CRC). However, a significant proportion of …
Enthalpy and entropy synergistic regulation–based programmable DNA motifs for biosensing and information encryption
LL Zheng, JZ Li, M Wen, D Xi, Y Zhu, Q Wei… - Science …, 2023 - science.org
Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of
information cryptography and biosensors. However, most conventional DNA regulation …
information cryptography and biosensors. However, most conventional DNA regulation …
Acetylated HOXB13 regulated super enhancer genes define therapeutic vulnerabilities of castration-resistant prostate cancer
Purpose: Androgen receptor (AR) antagonism is exacerbated by HOXB13 in castration-
resistant prostate cancers (CRPC). However, it is unclear when and how HOXB13 primes …
resistant prostate cancers (CRPC). However, it is unclear when and how HOXB13 primes …
Interfacial water confers transcription factors with dinucleotide specificity
Transcription factors (TFs) recognize specific bases within their DNA-binding motifs, with
each base contributing nearly independently to total binding energy. However, the energetic …
each base contributing nearly independently to total binding energy. However, the energetic …
Bispecific forkhead transcription factor FoxN3 recognizes two distinct motifs with different DNA shapes
Transcription factors (TFs) control gene expression by binding DNA recognition sites in
genomic regulatory regions. Although most forkhead TFs recognize a canonical forkhead …
genomic regulatory regions. Although most forkhead TFs recognize a canonical forkhead …
DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues
Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among
eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with …
eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with …