Cargando…

CCIP: predicting CTCF-mediated chromatin loops with transitivity

MOTIVATION: CTCF-mediated chromatin loops underlie the formation of topological associating domains and serve as the structural basis for transcriptional regulation. However, the formation mechanism of these loops remains unclear, and the genome-wide mapping of these loops is costly and difficult. M...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wang, Weibing, Gao, Lin, Ye, Yusen, Gao, Yong
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Original Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8665748/ https://www.ncbi.nlm.nih.gov/pubmed/34289010 http://dx.doi.org/10.1093/bioinformatics/btab534

Ejemplares similares

Predicting CTCF-mediated chromatin loops using CTCF-MP
por: Zhang, Ruochi, et al.
Publicado: (2018)

CTCF-mediated chromatin loops enclose inducible gene regulatory domains
por: Oti, Martin, et al.
Publicado: (2016)

Identification of chromatin loops from Hi-C interaction matrices by CTCF–CTCF topology classification
por: Galan, Silvia, et al.
Publicado: (2022)

CTCF and cohesin regulate chromatin loop stability with distinct dynamics
por: Hansen, Anders S, et al.
Publicado: (2017)

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention
por: Pugacheva, Elena M., et al.
Publicado: (2020)

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops
por: Guo, Yu, et al.
Publicado: (2018)

CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells
por: Handoko, Lusy, et al.
Publicado: (2011)

CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates
por: Lee, Ryanggeun, et al.
Publicado: (2021)

Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling
por: Tark-Dame, Mariliis, et al.
Publicado: (2014)

Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features
por: Kai, Yan, et al.
Publicado: (2018)

8-oxodG accumulation within super-enhancers marks fragile CTCF-mediated chromatin loops
por: Scala, Giovanni, et al.
Publicado: (2022)

Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
por: Szczepińska, Teresa, et al.
Publicado: (2021)

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
por: Pękowska, Aleksandra, et al.
Publicado: (2018)

MYC reshapes CTCF-mediated chromatin architecture in prostate cancer
por: Wei, Zhao, et al.
Publicado: (2023)

CTCF-mediated chromatin looping in EGR2 regulation and SUZ12 recruitment critical for peripheral myelination and repair
por: Wang, Jincheng, et al.
Publicado: (2020)

Correction: Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling
Publicado: (2016)

CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin
por: Ohlsson, Rolf, et al.
Publicado: (2010)

Prediction of CTCF loop anchor based on machine learning
por: Zhang, Xiao, et al.
Publicado: (2023)

CTCF, Cohesin, and Chromatin in Human Cancer
por: Song, Sang-Hyun, et al.
Publicado: (2017)

Loop competition and extrusion model predicts CTCF interaction specificity
por: Xi, Wang, et al.
Publicado: (2021)

Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver
por: Matthews, Bryan J, et al.
Publicado: (2018)

Imprinting at the PLAGL1 domain is contained within a 70-kb CTCF/cohesin-mediated non-allelic chromatin loop
por: Iglesias-Platas, Isabel, et al.
Publicado: (2013)

Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer
por: Cheng, Jessica, et al.
Publicado: (2022)

An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis
por: Li, Jiao, et al.
Publicado: (2019)

The structural basis for cohesin-CTCF anchored loops
por: Li, Yan, et al.
Publicado: (2020)

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin(STAG1) from WAPL
por: Wutz, Gordana, et al.
Publicado: (2020)

CTCF and Its Multi-Partner Network for Chromatin Regulation
por: Del Moral-Morales, Aylin, et al.
Publicado: (2023)

CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion
por: Davidson, Iain F., et al.
Publicado: (2023)

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
por: Beagan, Jonathan A., et al.
Publicado: (2017)

Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries
por: Islam, Zubairul, et al.
Publicado: (2023)

Role of LDB1 in the transition from chromatin looping to transcription activation
por: Krivega, Ivan, et al.
Publicado: (2014)

Acute depletion of CTCF rewires genome-wide chromatin accessibility
por: Xu, Beisi, et al.
Publicado: (2021)

CTCF looping is established during gastrulation in medaka embryos
por: Nakamura, Ryohei, et al.
Publicado: (2021)

Defining the multivalent functions of CTCF from chromatin state and three-dimensional chromatin interactions
por: Lu, Yiming, et al.
Publicado: (2016)

A CTCF-Binding Element and Histone Deacetylation Cooperatively Maintain Chromatin Loops, Linking to Long-Range Gene Regulation in Cancer Genomes
por: Tang, Ran, et al.
Publicado: (2022)

CTCF shapes chromatin structure and gene expression in health and disease
por: Dehingia, Bondita, et al.
Publicado: (2022)

Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping
por: Kernohan, Kristin D., et al.
Publicado: (2014)

Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo
por: Hanssen, Lars L P, et al.
Publicado: (2017)

Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding
por: Kadota, Shinichi, et al.
Publicado: (2020)

CTCF Mediates Replicative Senescence Through POLD1
por: Hou, Yuli, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_8uumi6anb6am44vuupflktod0i