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   Articles with "transcription start" as a keyword



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A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number‐dependent manner

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recommendations! 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.

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recommendations! 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.

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recommendations! 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

Transcription start sites experience a high influx of heritable variants fueled by early development

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recommendations! Published in 2025 at "Nature Communications"

DOI: 10.1038/s41467-025-66201-0

Abstract: Mutations drive evolution and genetic diversity, with the most consequential mutations occurring in coding exons and regulatory regions. However, the impact of transcription on germline mutagenesis remains poorly understood. Here, we identify a mutational hotspot… read more here.

Keywords: transcription start; start sites; germline; mutational hotspot ... See more keywords

Genome level identification of transcription start sites by nanoCAGE sequence in soybean

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recommendations! Published in 2025 at "Scientific Data"

DOI: 10.1038/s41597-025-06003-7

Abstract: Identification of transcription start sites (TSSs) of genes is critical for understanding promoter architecture and transcription initiation. A well-characterized and widely used method to determine TSSs is Cap Analysis of Gene Expression (CAGE). CAGE has… read more here.

Keywords: transcription start; start sites; soybean; identification transcription ... See more keywords
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A two-stream convolutional neural network for microRNA transcription start site feature integration and identification

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recommendations! 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

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recommendations! 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

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recommendations! 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

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recommendations! 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.

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recommendations! 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

How to recover from a bad start: adaptation of HIV-1 transcription start site mutants during serial passaging in culture

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recommendations! Published in 2025 at "Journal of Virology"

DOI: 10.1128/jvi.00159-25

Abstract: ABSTRACT HIV-1 uses neighboring sequences as transcription start sites and generates multiple unspliced transcripts, including two major transcripts with three guanosines (3G) or one guanosine (1G) at the 5′ end. Although only differing by 2-nt,… read more here.

Keywords: replication; transcription start; hiv; culture ... See more keywords