@CTCF_Papers

PubMed bot reporting all CTCF papers. Maintained by @TeifLab. Also see @TF_binding_bot, @Nucleosome_Bot, @generegulation

generegulation.org
Joined January 2016
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Excited to share our latest study published in Nucleic Acids Research: academic.oup.com/nar/article… It’s the cover story for Issue #12! We drew inspiration from Greek mythology to illustrate CTCF’s constant struggle in shaping the 3D genome architecture.
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Gene Regulation@generegulation3 Jan 2025
Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions [Liu et al, 2024] nature.com/articles/s41467-0… ▶️At one-dimensional level - modes of TF co-occupancy ▶️At pairwise contact level - multiway chromatin interactions of different TFs
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CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation biorxiv.org/content/10.1101/…

CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned...

CTCF binding sites serve as anchors for the 3D chromatin architecture in vertebrates. The functionality of these anchors is influenced by the residence time of CTCF on chromatin, which is determined...

biorxiv.org
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Our new CTCF breakthrough ms has been posted today at doi.org/10.1101/2024.09.25.6… with the following Graphical Abstract:
Victor V. Lobanenkov@boris_ctcf26 Sep 2024
⚠️ CTCF binding landscape is established by the epigenetic status of the nucleosome well-positioned relative to CTCF motif orientation BioRxiv Sep 26, Md Tajmul et al with Vladimir B. Teif, Victor Lobanenkov & Elena Pugacheva doi.org/10.1101/2024.09.25.6… biorxiv.org/content/10.1101/…
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Jane Skok@jane_skok14 Aug 2024
Factors that determine cell type–specific CTCF binding in health and d... sciencedirect.com/science/ar…
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Karsten Rippe@KarstenRippe7 Aug 2024
1/ 🤔 Do #chromatinlooping-mediated promoter-#enhancer interactions drive gene expression? Or is the local enrichment of transcription factors into hubs/#condensates the key factor? Our AC/DC model of gene regulation at bioRxiv doi.org/10.1101/2024.08.03.6… provides a new view on this.
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Teif Lab@TeifLab31 Jul 2024
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_…
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Registration (free!) and abstract submission now open! Please, spread the word. gate.essex.ac.uk/
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Gene Regulation@generegulation2 Jul 2024
Nucleus is looking for a new Editor-in-Chief. Nucleus is a fully Open Access journal by @tandfonline. Application deadline October 18, 2024 Further information including requirements and application process can be found here: think.taylorandfrancis.com/e…
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Denis Duboule@Duboule20 Feb 2024
The amazing coincidence between the topology of CTCF binding sites within Hox clusters and two major transitions in the vertebrate body plan. 🙏 Hocine @Hocine_Rekaik @cdf1530 @the_Node @CTCF_Papers #FlattenedEmbryo sciencedirect.com/science/ar…
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Happy to share! Our latest publication in Genome Biology unveils how BORIS/CTCFL epigenetically reprograms transcriptionally inactive intronic CTCF sites into alternative promoters: genomebiology.biomedcentral.…

BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional...

Genome Biology - Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little...

link.springer.com
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Locus folding mechanisms determine modes of antigen receptor gene assembly dlvr.it/T16hBL

Locus folding mechanisms determine modes of antigen receptor gene assembly - PubMed

The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and...

pubmed.ncbi.nlm.nih.gov
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DNA-sequence and epigenomic determinants of local rates of transcription elongation dlvr.it/T15vcC

DNA-sequence and epigenomic determinants of local rates of transcription elongation - PubMed

Across all branches of life, transcription elongation is a crucial, regulated phase in gene expression. Many recent studies in eukaryotes have focused on the regulation of promoter-proximal pausing...

pubmed.ncbi.nlm.nih.gov
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LncRNA SLC7A11-AS1 stabilizes CTCF by inhibiting its UBE3A-mediated ubiquitination to promote melanoma metastasis dlvr.it/T15vbR

LncRNA SLC7A11-AS1 stabilizes CTCF by inhibiting its UBE3A-mediated ubiquitination to promote...

Malignant melanoma (MM) is one of the most aggressive types of skin cancer. Long non-coding RNAs (lncRNAs) are important regulatory factors in the pathogenesis of various diseases. Here, we found...

pubmed.ncbi.nlm.nih.gov
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Benchmarking DNA binding affinity models using allele-specific transcription factor binding data dlvr.it/T15vXh

Benchmarking DNA binding affinity models using allele-specific transcription factor binding data -...

Transcription factors (TFs) bind to DNA in a highly sequence-specific manner. This specificity can manifest itself in vivo at heterozygous loci as a difference in TF occupancy between the two...

pubmed.ncbi.nlm.nih.gov
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Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies dlvr.it/T12ZF1

Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies -...

Dementia with Lewy bodies (DLB) is a common form of dementia in the elderly population. We performed genome-wide DNA methylation mapping of cerebellar tissue from pathologically confirmed DLB cases...

pubmed.ncbi.nlm.nih.gov
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CTCF regulates hepatitis B virus cccDNA chromatin topology dlvr.it/T0ynnV

CTCF regulates hepatitis B virus cccDNA chromatin topology - PubMed

Hepatitis B Virus (HBV) is a small DNA virus that replicates via an episomal covalently closed circular DNA (cccDNA) that serves as the transcriptional template for viral mRNAs. The host protein,...

pubmed.ncbi.nlm.nih.gov
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Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization dlvr.it/T0yS21

Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of...

Macrophages display extreme plasticity, and the mechanisms and applications of polarization and de-/repolarization of macrophages have been extensively investigated. However, the regulation of...

pubmed.ncbi.nlm.nih.gov
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A study on genotypes and phenotypes of short stature caused by epigenetic modification gene variants dlvr.it/T0xMQ8

A study on genotypes and phenotypes of short stature caused by epigenetic modification gene...

Mendelian disorders of the epigenetic machinery (MDEMs) are caused by genetic mutations, a considerable fraction of which are associated with epigenetic modification. These MDEMs exhibit phenotypic...

pubmed.ncbi.nlm.nih.gov
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The counterpart congenital overgrowth syndromes Beckwith-Wiedemann Syndrome in human and large offspring syndrome in bovine involve alterations in DNA methylation, transcription, and chromatin configuration dlvr.it/T0xMQ5

Beckwith-Wiedemann syndrome and large offspring syndrome involve alterations in methylome, transc...

Beckwith-Wiedemann Syndrome (BWS) is the most common epigenetic overgrowth syndrome, caused by epigenetic alterations on chromosome 11p15. In ∼50% of patients with BWS, the imprinted region KvDMR1...

pubmed.ncbi.nlm.nih.gov
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