Results 71 to 80 of about 928,240 (334)

Identification of H3K4me1-associated proteins at mammalian enhancers. [PDF]

, 2017
Enhancers act to regulate cell-type-specific gene expression by facilitating the transcription of target genes. In mammalian cells, active or primed enhancers are commonly marked by monomethylation of histone H3 at lysine 4 (H3K4me1) in a cell-type ...
Albuquerque, Claudio P, Corbett, Kevin D, Ge, Kai, Hsia, Judy E, Huang, Hui, Lee, Ah Young, Local, Andrea, Ren, Bing, Shiau, Andrew K, Singh, Namit, Wang, Chaochen, Wang, Dong, Wang, Wei, Zhou, Huilin   +13 more
core   +2 more sources

CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection

Scientific Reports, 2020
ChIP-seq is one of the core experimental resources available to understand genome-wide epigenetic interactions and identify the functional elements associated with diseases.
Dongpin Oh, J. Strattan, J. Hur, José Bento, A. Urban, Giltae Song, J. Cherry   +6 more
semanticscholar   +1 more source

Circular RNA expression landscapes in myelodysplastic neoplasms: Associations with mutational signatures and disease progression

Molecular Oncology, EarlyView.
In this explorative study, the abundance of circular RNA molecules in bone marrow stem cells was found to be elevated in patients with high‐risk myelodysplastic neoplasms, and to be associated with an increased risk of progression to acute myeloid leukemia.
Eileen Wedge, Morten Tulstrup, Gabriele Todisco, Pedro Moura, Christophe Côme, Jakob Werner Hansen, Jakob Schmidt Jespersen, Balthasar Schlotmann, Maria Creignou, Mette Dahl, Claudia Schöllkopf, Klas Raaschou‐Jensen, Krister Wennerberg, Bo Porse, Joachim Weischenfeldt, Eva Hellström‐Lindberg, Lasse Sommer Kristensen, Kirsten Grønbæk   +17 more
wiley   +1 more source

Tissue-Specific In Vivo Biotin Chromatin Immunoprecipitation with Sequencing in Zebrafish and Chicken

STAR Protocols, 2020
Summary: Chromatin immunoprecipitation with sequencing (ChIP-seq) has been instrumental in understanding transcription factor (TF) binding during gene regulation.
Martyna Lukoseviciute, Irving T.C. Ling, Upeka Senanayake, Ivan Candido-Ferreira, Gunes Taylor, Ruth M. Williams, Tatjana Sauka-Spengler   +6 more
doaj   +1 more source

Practical guidelines for the comprehensive analysis of ChIP-seq data. [PDF]

PLoS Computational Biology, 2013
Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE)
Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang   +8 more
doaj   +1 more source

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

Antibody performance in ChIP-sequencing assays: From quality scores of public data sets to quantitative certification [version 2; referees: 2 approved]

F1000Research, 2016
We have established a certification system for antibodies to be used in chromatin immunoprecipitation assays coupled to massive parallel sequencing (ChIP-seq).
Marco-Antonio Mendoza-Parra, Vincent Saravaki, Pierre-Etienne Cholley, Matthias Blum, Benjamin Billoré, Hinrich Gronemeyer   +5 more
doaj   +1 more source

Phylogenetic Analysis of Cell Types using Histone Modifications

, 2013
In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the ...
Bucher, Philipp, Lin, Yu, Moret, Bernard M. E., Nair, Nishanth Ulhas   +3 more
core   +1 more source

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

Nucleic Acids Res., 2016
The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive.
Ke-ren Zhou, Shun Liu, Wen-Ju Sun, Lingling Zheng, Hui Zhou, Jianhua Yang, L. Qu   +6 more
semanticscholar   +1 more source

CCDC80 suppresses high‐grade serous ovarian cancer migration via negative regulation of B7‐H3

Molecular Oncology, EarlyView.
PAX8 is a lineage‐specific master regulator of transcription in high‐grade serous ovarian cancer (HGSC) progression. We show for the first time that PAX8 facilitates proliferation and metastasis by repressing the cell autonomous tumor suppressor CCDC80 and inducing B7‐H3 expression.
Aya Saleh, Nitzan Medina‐Itzhaki, Milena Chekov, Eden Gal‐Swisa, Roba Gabesh‐Wahabi, Inbar Savyon, Inna Naroditsky, Hilary A. Kenny, Basem Fares, Lina Korsensky, Einav Girsh, Liron Berger, Ruth Perets   +12 more
wiley   +1 more source