A biallelically active embryonic enhancer dictates GNAS imprinting through allele-specific conformations by Yorihiro Iwasaki, Monica Reyes, Harald Jüppner, Murat Bastepe

“…Here, we show that the STX16-ICR forms different chromatin conformations with each GNAS parental allele and enhances two GNAS promoters in human embryonic stem cells. …”
Get full text

Where Environment Meets Cognition: A Focus on Two Developmental Intellectual Disability Disorders by I. De Toma, L. Manubens Gil, S. Ossowski, M. Dierssen

“…Epigenetic treatments act in a context specific manner, targeting different regions based on cell and state specific chromatin accessibility, facilitating the establishment of the lost balance. …”
Get full text

Deciphering the effect of UM171 on human hematopoietic progenitor cell fate through clonal analysis by Patrick Coulombe, Elisa Tomellini, Jalila Chagraoui, Nadine Mayotte, Guy Sauvageau

“…This can be achieved via exposure to UM171 which leads to the degradation of chromatin modifiers and prevents the loss of key epigenetic marks. …”
Get full text

CHD7 Regulates Osteogenic Differentiation of Human Dental Follicle Cells via PTH1R Signaling by Caojie Liu, Qiwen Li, Qingyue Xiao, Ping Gong, Ning Kang

“…Chromodomain helicase DNA-binding protein 7 (CHD7) is an ATP-dependent chromatin remodeling enzyme, functioning as chromatin reader to conduct epigenetic modification. …”
Get full text

PIWI proteins and piRNAs: key regulators of stem cell biology by Fernando Claro-Linares, Patricia Rojas-Ríos

“…Precisely, in GSCs, PIWI proteins and piRNAs regulate gene expression by modulating chromatin states and directly influencing mRNA translation. …”
Get full text

Methylated H3K4, a transcription-associated histone modification, is involved in the DNA damage response pathway. by David Faucher, Raymund J Wellinger

“…Eukaryotic genomes are associated with a number of proteins such as histones that constitute chromatin. Post-translational histone modifications are associated with regulatory aspects executed by chromatin and all transactions on genomic DNA are dependent on them. …”
Get full text

Identification of a distal enhancer of Ucp1 essential for thermogenesis and mitochondrial function in brown fat by Duo Su, Tingting Jiang, Yulong Song, Die Li, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Li Li, Hongping Zhang, Linjie Wang

“…However, the molecular mechanisms by which enhancer–promoter chromatin interactions control Ucp1 transcriptional regulation in brown adipose tissue (BAT) are unclear. …”
Get full text

Integrated analysis of ATAC-seq and RNA-seq reveals ADSCP2 regulates oxidative phosphorylation pathway in hypertrophic scar fibroblasts by Qian Li, Zhe Quan, Ling Chen, Yiliang Yin, Xin Chen, Jingyun Li

“…Consequently, this study sought to elucidate the potential mechanism associated with ADSCP2 by examining genome-wide transcriptional alterations and changes in chromatin accessibility in fibroblasts. This was achieved through the integrated analysis of assay for transposase accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq). …”
Get full text

KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition by Deniz Gökbuget, Liana Goehring, Ryan M. Boileau, Kayla Lenshoek, Tony T. Huang, Robert Blelloch

“…Using machine learning, we quantify 21 chromatin features predicting local RT and RT changes during differentiation in embryonic stem cells (ESCs). …”
Get full text

Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells. by Karsten Jürchott, Ralf-Jürgen Kuban, Till Krech, Nils Blüthgen, Ulrike Stein, Wolfgang Walther, Christian Friese, Szymon M Kiełbasa, Ute Ungethüm, Per Lund, Thomas Knösel, Wolfgang Kemmner, Markus Morkel, Johannes Fritzmann, Peter M Schlag, Walter Birchmeier, Tammo Krueger, Silke Sperling, Christine Sers, Hans-Dieter Royer, Hanspeter Herzel, Reinhold Schäfer

“…We recognized E2F and NFY transcription factor binding sites as prevalent motifs in those pathway-responsive genes and confirmed the predicted regulatory role of Y-box binding protein 1 (YBX1) by reporter gene, gel shift, and chromatin immunoprecipitation assays. We also validated the MAPK-dependent gene signature in colorectal cancers and provided evidence for the association of YBX1 with poor prognosis in colorectal cancer patients. …”
Get full text

Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls by Kashif Hameed Anjum, Asif Nadeem, Maryam Javed, Hafiz Ishfaq Ahmad, Amjad Riaz, Wasim Shehzad, Jahanzaib Azhar, Muhammad Fahad Bhutta

“…Transition nuclear proteins (TNPs), the principal proteins identified in the condensing spermatids chromatin, have been found to play a key role in histone displacement and chromatin condensation during mammalian spermatogenesis. …”
Get full text

Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis by Tanishq Sahu, Ruchi Yadav

“…Context: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the central system in epigenomic exploration. …”
Get full text

The Impact of Epigenetics on the Pathophysiology of Type 2 Diabetes and Associated Nephropathic Complications by Amit Mukherjee, Tanusree Debbarman, Basu D. Banerjee, Sheelu S. Siddiqi

“…Various epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA regulation, drive cell dysfunction, inflammation, and fibrosis, aggravating diabetes and its complications. …”
Get full text

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics by Honggui Wu, Maoxu Wang, Yinghui Zheng, X. Sunney Xie

“…Abstract Single-cell three-dimensional (3D) genome techniques have advanced our understanding of cell-type-specific chromatin structures in complex tissues, yet current methodologies are limited in cell throughput. …”
Get full text

Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis by Alireza Lorzadeh, George Ye, Sweta Sharma, Unmesh Jadhav

“…Abstract Transcription factors guide tissue development by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of transcription factors. …”
Get full text

In vivo Study of the Histone Chaperone Activity of Nucleolin by FRAP by Xavier Gaume, Karine Monier, Françoise Argoul, Fabien Mongelard, Philippe Bouvet

“…Thus, in live cells, nucleolin could play a role in chromatin accessibility by its histone chaperone and co-remodeling activities.…”
Get full text

Impaired ARID1A expression attenuated the immune response in gastric cancer via histone acetylation by Yu Tang, Ruizhi Zhang, Gan Mao, Chong Li, Yisong Gao, Xuebing Zhou, Wenxiang Nie, Tianyu Song, Suao Liu, Kaixiong Tao, Peng Zhang, Wei Li

“…Real-time PCR was employed for gene expression analysis, while chromatin immunoprecipitation was used to identify transcriptional regulation on target genes. …”
Get full text

Ubiquitin Proteasome System in Stress and Disease by Dmitry Karpov, Michael H. Glickman, Shoshana Bar-Nun, Philip Coffino

Get full text

Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize by Yi Luo, Hang Zhai, Xiu Zhong, Bo Yang, Yang Xu, Tianhong Liu, Qi Wang, Yang Zhou, Yan Mao, Yaxi Liu, Qi Tang, Yanli Lu, Yao Wang, Jie Xu

“…To explore the regulatory characteristics of the CNS identified, the flanking regions of CNS were compared with the peaks called using both transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) data of histone modifications. …”
Get full text

JUNB O‐GlcNAcylation‐Mediated Promoter Accessibility of Metabolic Genes Modulates Distinct Epithelial Lineage in Pulmonary Fibrosis by Marie‐Therese Bammert, Meshal Ansari, Leoni Haag, Zuhdi Ahmad, Victoria Schröder, Joseph Birch, Diana Santacruz, Werner Rust, Coralie Viollet, Benjamin Strobel, Alec Dick, Florian Gantner, Holger Schlüter, Fidel Ramirez, Muriel Lizé, Matthew J. Thomas, Huy Q. Le

“…This remodeling is characterized by an increase in chromatin accessibility, particularly at JUNB motif‐enriched promoter regions proximal to transcription start sites of metabolic and pro‐fibrotic genes. …”
Get full text