Papers on transcription factor binding #TFbinding. Maintained by @TeifLab. Also see @nucleosome_bot, @CTCF_papers, @DNAbinding, @cfDNA_papers, @generegulation
Animal Stem cells probably appeared 700-800 million years ago. We found that two key molecules that make our stem cells the way they are even older than that as they even existed before the evolution of animals. 1/n
Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors https://t.co/yXjLlDl1Xo
▶️This preprint provides a summary of the release of a bunch of new preprints by the Codebook Consortium (see three posts below). #TFbinding
Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors (Vorontsov et al, 2024) https://t.co/wbw2KLgmpY
▶️Codebook: 4,237 experiments, 394 human proteins
▶️Codebook Motif Explorer https://t.co/2EKoJC11hQ
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors (Jolma et al., 2024) https://t.co/A7847MTFoB
▶️TFs possess sufficient intrinsic specificity to independently delineate cellular targets
Extensive binding of uncharacterized human transcription factors to genomic dark matter (Razavi et al., 2024) https://t.co/lBkj8tTSnH
▶️166 uncharacterized human TFs
▶️"Dark TFs", mainly bind closed chromatin enriched for transposable elements
▶️Some Dark TFs contain KRAB domain
An atlas of conserved transcription factor binding sites reveals the cell type-resolved gene regulatory landscape of flowering plants https://t.co/jnbYw5K0wQ #biorxiv_genomic
CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation https://t.co/FlDw62Vwdj
The registration deadline for our FREE conference in Colchester is prolonged until 1st September. The conference itself is on 16th September. Short talk slots available, hurry up!
We have an opening for a three-year postdoctoral position for a researcher with expertise in machine learning and genome bioinformatics, to work on cancer diagnostics (liquid biopsies). Please apply here: https://t.co/wT5EuK5GmS
We are organising a conference "Genomics in Ageing and Disease", 16th September 2024, University of Essex, Colchester. More details soon https://t.co/avfiR4gCQa
Our paper on nucleosome repositioning in breast cancer is now published in Clinical Epigenetics! https://t.co/nCEWTcRzPO
▶️Nucleosome gain marks deregulated TFs
▶️Shorter distances between nucleosomes in cancer
▶️NRL affected by gene expression, methylation, H1 histones, repeats
Our work on the identification of new pioneer transcription factors is out, in collaboration with @YunhuiP@DavidLandsman@TeifLab
https://t.co/cBXl0CEEZP
D-box-binding protein alleviates vascular calcification in rats with chronic kidney disease by activating microRNA-195-5p and downregulating cyclin D1 https://t.co/3JDCGKeSjX