TF binding papers 📚 NucPosDB database

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 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

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