Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide DOI Creative Commons
Magda Kopczyńska, Upasana Saha,

Anastasiia Romanenko

и другие.

Nucleic Acids Research, Год журнала: 2024, Номер unknown

Опубликована: Дек. 24, 2024

Abstract Defining the beginning of a eukaryotic protein-coding gene is relatively simple. It corresponds to first ribonucleotide incorporated by RNA polymerase II (Pol II) into nascent molecule. This nucleotide protected capping and maintained in mature messenger (mRNA). However, higher eukaryotes, end mRNA separated from sites transcription termination hundreds thousands base pairs. Currently used genomic annotations only take account transcript – where pre-mRNA cleavage occurs, while regions which terminates are unannotated. Here, we describe evidence for marker termination, could be widely applicable studies. Pol can determined genome-wide detecting phosphorylated on threonine 4 its C-terminal domain CTD-T4ph). this state pauses before leaving DNA template. Up date potent mark has been underused because place role scattered across multiple publications. We summarize observations regarding CTD-T4ph present bioinformatic analyses that further support as global animals.

Язык: Английский

AlphaPulldown2 – A General Pipeline for High-Throughput Structural Modeling DOI Creative Commons
Dmitry Molodenskiy, Valentin Maurer, Dingquan Yu

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 3, 2024

Abstract AlphaPulldown2 streamlines protein structural modeling by automating workflows, improving code adaptability, and optimizing data management for large-scale applications. It introduces an automated Snakemake pipeline, compressed storage, support additional backends like UniFold AlphaLink2, a range of other improvements. These upgrades make versatile platform predicting both binary interactions complex multi-unit assemblies. Availability is freely available at https://github.com/KosinskiLab/AlphaPulldown .

Язык: Английский

Процитировано

0
Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide DOI Creative Commons
Magda Kopczyńska, Upasana Saha,

Anastasiia Romanenko

и другие.

Nucleic Acids Research, Год журнала: 2024, Номер unknown

Опубликована: Дек. 24, 2024

Abstract Defining the beginning of a eukaryotic protein-coding gene is relatively simple. It corresponds to first ribonucleotide incorporated by RNA polymerase II (Pol II) into nascent molecule. This nucleotide protected capping and maintained in mature messenger (mRNA). However, higher eukaryotes, end mRNA separated from sites transcription termination hundreds thousands base pairs. Currently used genomic annotations only take account transcript – where pre-mRNA cleavage occurs, while regions which terminates are unannotated. Here, we describe evidence for marker termination, could be widely applicable studies. Pol can determined genome-wide detecting phosphorylated on threonine 4 its C-terminal domain CTD-T4ph). this state pauses before leaving DNA template. Up date potent mark has been underused because place role scattered across multiple publications. We summarize observations regarding CTD-T4ph present bioinformatic analyses that further support as global animals.

Язык: Английский

Процитировано

0