Cis-regulatory elements (CREs) and transcription factors (TFs) associated with them determine temporal and spatial domains of gene expression. Therefore, identification of these CREs and TFs is crucial to elucidating transcriptional programs across taxa. With chromatin accessibility facilitating transcription factor access to DNA, the identification of regions of open chromatin sheds light both on the function of the regulatory elements and their evolution, thus allowing the recognition of potential CREs. Buenrostro and colleagues have developed a novel method for exploring chromatin accessibility: assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), which can be used for the purpose of identifying putative CREs. This method was shown to have considerable advantages when compared to traditional methods such as sequence conservation analyses or functional assays. Here we present the adaptation of the ATAC-seq method to echinoderm species and discuss how it can be used for CRE discovery.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1007/978-1-0716-0974-3_16 | DOI Listing |
Cell Death Dis
January 2025
Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
Prostate cancer is a heterogeneous disease with a slow progression and a highly variable clinical outcome. The tumor suppressor genes PTEN and TP53 are frequently mutated in prostate cancer and are predictive of early metastatic dissemination and unfavorable patient outcomes. The progression of solid tumors to metastasis is often associated with increased cell plasticity, but the complex events underlying TP53-loss-induced disease aggressiveness remain incompletely understood.
View Article and Find Full Text PDFInt Rev Cell Mol Biol
January 2025
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States. Electronic address:
Acute myeloid leukemia (AML) is a complex cancer, yet advances in recent years from integrated genomics methods have helped improve diagnosis, treatment, and means of patient stratification. A recent example of a powerful, multimodal method is DOGMA-seq, which can measure chromatin accessibility, gene expression, and cell-surface protein levels from the same individual cell simultaneously. Previous bimodal single-cell techniques, such as CITE-seq (Cellular indexing of transcriptomes and epitopes), have only permitted the transcriptome and cell-surface protein expression measurement.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement/Jiangsu Province Engineering Research Center of Modern Strawberry Industry/Zhongshan Biological Breeding Laboratory, 50 Zhonglin Road, Nanjing 210014, China.
Light is an important environmental factor affecting the ripening and quality of strawberry fruit. Previous studies have shown that red light treatment can promote strawberry ripening. Gene expression is closely associated with chromatin openness, and changes in chromatin accessibility are crucial for the binding of transcription factors to downstream regulatory sequences.
View Article and Find Full Text PDFAnimals (Basel)
January 2025
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
Feed efficiency (FE) is a crucial trait in pig production that influences both economic viability and environmental sustainability. The jejunum, an essential organ for nutrient absorption, plays a significant role in determining FE by affecting how pigs process and utilize feed. To explore the genetic and regulatory mechanisms behind FE, we conducted an integrative multi-omics study using RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) on pigs with high and low FE.
View Article and Find Full Text PDFBMC Genomics
January 2025
Department of Vascular Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China.
Background: Vascular cognitive impairment (VCI) is a significant contributor to dementia, yet the precise mechanisms underlying the cognitive decline associated with chronic cerebral hypoperfusion (CCH) remain unclear. This study investigated the molecular and epigenetic changes in the striatum, a brain region critical for motor function and cognition, following chronic hypoperfusion using a bilateral common carotid artery stenosis (BCAS) model in mice.
Methods: RNA-seq was utilized to identify differentially expressed genes (DEGs) associated with hypoperfusion.
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!