A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number‐dependent manner
Sign Up to like & getrecommendations! Published in 2020 at "Human Mutation"
DOI: 10.1002/humu.23974
Abstract: Minisatellites, also called variable number of tandem repeats (VNTRs), are a class of repetitive elements that may affect gene expression at multiple levels and have been correlated to disease. Their identification and role as expression… read more here.
Keywords: start site; number; repeat number; expression ... See more keywords
Chd1p recognizes H3K36Ac to maintain nucleosome positioning near the transcription start site.
Sign Up to like & getrecommendations! Published in 2018 at "Biochemical and biophysical research communications"
DOI: 10.1016/j.bbrc.2018.07.025
Abstract: In Saccharomyces cerevisiae, the ATP-dependent chromatin remodeler, Chd1p, globally affects nucleosome positioning at coding regions, where nucleosomes are specifically and directionally aligned with respect to the transcription start site (TSS). Various auxiliary domains of remodelers… read more here.
Keywords: start site; chd1p; h3k36ac; transcription start ... See more keywords
refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of molecular biology"
DOI: 10.1016/j.jmb.2019.04.045
Abstract: Transcription starts at genomic positions called transcription start sites (TSSs), producing RNAs, and is mainly regulated by genomic elements and transcription factors binding around these TSSs. This indicates that TSSs may be a better unit… read more here.
Keywords: transcription; human mouse; reference; start sites ... See more keywords
A two-stream convolutional neural network for microRNA transcription start site feature integration and identification
Sign Up to like & getrecommendations! Published in 2021 at "Scientific Reports"
DOI: 10.1038/s41598-021-85173-x
Abstract: MicroRNAs (miRNAs) play important roles in post-transcriptional gene regulation and phenotype development. Understanding the regulation of miRNA genes is critical to understand gene regulation. One of the challenges to study miRNA gene regulation is the… read more here.
Keywords: condition specific; mirna; mirna tss; specific mirna ... See more keywords
Computational annotation of miRNA transcription start sites
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbz178
Abstract: Abstract Motivation MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in gene regulation and phenotype development. The identification of miRNA transcription start sites (TSSs) is critical to understand the functional roles of miRNA… read more here.
Keywords: transcription; annotation; start sites; mirna tsss ... See more keywords
Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac1126
Abstract: Abstract Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this… read more here.
Keywords: syd brm; chromatin remodelers; spt6l; chromatin ... See more keywords
The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac826
Abstract: Abstract Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically… read more here.
Keywords: positioning transcription; swi snf; transcription; nucleosome positioning ... See more keywords
Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites.
Sign Up to like & getrecommendations! Published in 2019 at "Genome research"
DOI: 10.1101/gr.240861.118
Abstract: Retroelement integration into host genomes affects both genome structure and function. A goal of a considerable number of investigations is to elucidate host features that influence insertion site selection. The retrotransposon Ty3 of Saccharomyces cerevisiae… read more here.
Keywords: targeting frequency; frequency; rna polymerase; start sites ... See more keywords
Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2022.1026847
Abstract: The transcriptional activity of Transposable Elements (TEs) has been involved in numerous pathological processes, including neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. The TE expression analysis from short-read sequencing technologies is,… read more here.
Keywords: level; expression analysis; expression; transcription start ... See more keywords
Using CRISPR/Cas9 genome editing in human iPSCs for deciphering the pathogenicity of a novel CCM1 transcription start site deletion
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.953048
Abstract: Cerebral cavernous malformations are clusters of aberrant vessels that can lead to severe neurological complications. Pathogenic loss-of-function variants in the CCM1, CCM2, or CCM3 gene are associated with the autosomal dominant form of the disease.… read more here.
Keywords: crispr cas9; deletion; cas9 genome; using crispr ... See more keywords