TF binding papers 📚 NucPosDB database
@TF_binding_bot
Papers on transcription factor binding #TFbinding. Maintained by @TeifLab. Also see @nucleosome_bot, @CTCF_papers, @DNAbinding, @cfDNA_papers, @generegulation
Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions [Liu et al, 2024] nature.com/articles/s4146… ▶️At one-dimensional level - modes of TF co-occupancy ▶️At pairwise contact level - multiway chromatin interactions of different TFs
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 biorxiv.org/content/10.110… ▶️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) biorxiv.org/content/10.110… ▶️Codebook: 4,237 experiments, 394 human proteins ▶️Codebook Motif Explorer mex.autosome.org
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors (Jolma et al., 2024) biorxiv.org/content/10.110… ▶️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) biorxiv.org/content/10.110… ▶️166 uncharacterized human TFs ▶️"Dark TFs", mainly bind closed chromatin enriched for transposable elements ▶️Some Dark TFs contain KRAB domain
Emerging links between phase separation and transcription factor haploinsufficiency [Reiner Veitia] cell.com/trends/genetic… #TFbinding
An atlas of conserved transcription factor binding sites reveals the cell type-resolved gene regulatory landscape of flowering plants biorxiv.org/cgi/content/sh… #biorxiv_genomic
CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation biorxiv.org/content/10.110…
Hurry up! Last day to submit abstract for "Genomics in Ageing and Disease" (Colchester, 16th September). Free Registration! Talks by @Peter_Fraser1, @_parker_aim, @GabriellaFicz, @EnrightAnton, @R_Rahbari, @ozgendeniz_, @jordanatbell, @sj_marzi & Essex PIs gate.essex.ac.uk
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 are organising a conference "Genomics in Ageing and Disease", 16th September 2024, University of Essex, Colchester. More details soon gate.essex.ac.uk
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: vacancies.essex.ac.uk/tlive_webrecru…
Registration (free!) and abstract submission now open! Please, spread the word. gate.essex.ac.uk
We are organising a conference "Genomics in Ageing and Disease", 16th September 2024, University of Essex, Colchester. More details soon gate.essex.ac.uk
The Genomics at Essex conference is back! We are working on it but you can check the latest news here and in gate.essex.ac.uk #gate2024
TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors genomebiology.biomedcentral.com/articles/10.11…
Our paper on nucleosome repositioning in breast cancer is now published in Clinical Epigenetics! …lepigeneticsjournal.biomedcentral.com/articles/10.11… ▶️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 elifesciences.org/articles/88936
Exploring Data-Driven Chemical SMILES Tokenization Approaches to Identify Key Protein-Ligand Binding Moieties dlvr.it/T1ByQF
Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells dlvr.it/T1ByKz
D-box-binding protein alleviates vascular calcification in rats with chronic kidney disease by activating microRNA-195-5p and downregulating cyclin D1 dlvr.it/T16blq