TF binding papers 📚 NucPosDB database

Papers on transcription factor binding #TFbinding. Maintained by @TeifLab. Also see @nucleosome_bot, @CTCF_papers, @DNAbinding, @cfDNA_papers, @generegulation

[Gene Regulation @generegulation]

Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions [Liu et al, 2024] https://t.co/4ycdplTA3o
▶️At one-dimensional level - modes of TF co-occupancy
▶️At pairwise contact level - multiway chromatin interactions of different TFs

[Ralf Jauch @jauchr]

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

[Gene Regulation @generegulation]

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

[Gene Regulation @generegulation]

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

[Gene Regulation @generegulation]

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

[Gene Regulation @generegulation]

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

[Gene Regulation @generegulation]

Emerging links between phase separation and transcription factor haploinsufficiency [Reiner Veitia] https://t.co/bVYClqYzXA #TFbinding

[bioRxiv Genomics @biorxiv_genomic]

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

[Elena Pugacheva @ElenaPugachev12]

CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation https://t.co/FlDw62Vwdj

[Gene Regulation @generegulation]

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 https://t.co/5AOJCDmzZf

[Teif Lab @TeifLab]

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!

[Teif Lab @TeifLab]

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

[Genomics at Essex @GenomicsAtEssex]

Registration (free!) and abstract submission now open! Please, spread the word.
https://t.co/WbJ1T7zzHE

[Teif Lab @TeifLab]

We are organising a conference "Genomics in Ageing and Disease", 16th September 2024, University of Essex, Colchester. More details soon https://t.co/avfiR4gCQa

[Gene Regulation @generegulation]

TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors https://t.co/3mL5RU8iTJ

[Teif Lab @TeifLab]

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

[Panchenko lab @AnnaPanchenko13]

Our work on the identification of new pioneer transcription factors is out, in collaboration with @YunhuiP @DavidLandsman @TeifLab
https://t.co/cBXl0CEEZP

[TF binding papers 📚 NucPosDB database @TF_binding_bot]

Exploring Data-Driven Chemical SMILES Tokenization Approaches to Identify Key Protein-Ligand Binding Moieties https://t.co/PqKJ3pZvMA

[TF binding papers 📚 NucPosDB database @TF_binding_bot]

Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells https://t.co/qV63MbLiZS

[TF binding papers 📚 NucPosDB database @TF_binding_bot]

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