Low-affinity binding sites and the transcription factor specificity paradox in eukaryotes
JF Kribelbauer, C Rastogi… - Annual review of cell …, 2019 - annualreviews.org
Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …
Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation
RR Catarino, A Stark - Genes & development, 2018 - genesdev.cshlp.org
Enhancers are important genomic regulatory elements directing cell type-specific
transcription. They assume a key role during development and disease, and their …
transcription. They assume a key role during development and disease, and their …
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
I Rauluseviciute, R Riudavets-Puig… - Nucleic Acids …, 2024 - academic.oup.com
Abstract JASPAR (https://jaspar. elixir. no/) is a widely-used open-access database
presenting manually curated high-quality and non-redundant DNA-binding profiles for …
presenting manually curated high-quality and non-redundant DNA-binding profiles for …
Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning
Protein–ligand interactions are increasingly profiled at high throughput using affinity
selection and massively parallel sequencing. However, these assays do not provide the …
selection and massively parallel sequencing. However, these assays do not provide the …
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Abstract JASPAR (http://jaspar. genereg. net) is an open-access database of curated, non-
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
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 …
HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors
We present a major update of the HOCOMOCO collection that provides DNA binding
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …
DeepDISOBind: accurate prediction of RNA-, DNA-and protein-binding intrinsically disordered residues with deep multi-task learning
Proteins with intrinsically disordered regions (IDRs) are common among eukaryotes. Many
IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported …
IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported …
Massively parallel assays and quantitative sequence–function relationships
JB Kinney, DM McCandlish - Annual review of genomics and …, 2019 - annualreviews.org
Over the last decade, a rich variety of massively parallel assays have revolutionized our
understanding of how biological sequences encode quantitative molecular phenotypes …
understanding of how biological sequences encode quantitative molecular phenotypes …
Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors
Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to
regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical …
regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical …