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Global investigation of RNA 3'end processing and transcription termination pathways: termination pathways

Publikation: Bog/antologi/afhandling/rapportPh.d.-afhandlingForskning

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Global investigation of RNA 3'end processing and transcription termination pathways : termination pathways. / Molska, Ewa.

2018. 142 s.

Publikation: Bog/antologi/afhandling/rapportPh.d.-afhandlingForskning

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@phdthesis{37a3ddf9c7174f7d8a2c75be2a5ed940,
title = "Global investigation of RNA 3'end processing and transcription termination pathways: termination pathways",
abstract = "RNA polymerases transcribe diverse classes of genes and the produced RNAs need to be targeted to their appropriate cognate biochemical maturation pathways. The vast majority of the human transcriptome consists of long non-coding RNAs (lncRNAs), which is a heterogeneous group of RNAs that is inadequately divided into classes based e.g. on length, stability and association with protein-coding genes. We reasoned that further classification based on biochemical properties, in this case transcription termination and the mechanistically coupled RNA 3{\textquoteright}-end processing, would enable a better understanding about the biogenesis and possible functionality of such transcripts. Many lncRNAs are short-lived, which makes them difficult to detect with standard methods. Therefore, we applied a specialized next generation sequencing protocol called transient transcriptome sequencing (TT-seq) that allows the study of transcription termination on genes encoding both stable and unstable transcripts. We successfully obtained TT-seq data enriched for unstable lncRNAs from human cells depleted of factors known to be involved in transcription termination and RNA 3{\textquoteright}-end processing. We developed a data-driven annotation protocol, which aided the discovery of transient RNA species and enabled determination of the pathways responsible for transcription termination on a multitude of genes. Our results demonstrate that genes corresponding to specific RNA classes do not pertain to one specific transcription termination pathway. For example, contrary to prediction, a subset of protein-coding genes utilise the machinery used by genes encoding U snRNAs. This same machinery is predominantly used by a class of lncRNA genes, encoding so-called PROMPTs, despite the presence of sequence elements predicted to guide the usage of the pathway mainly used by protein-coding genes. Thus, our results underscore the importance of functional studies over bioinformatic prediction. Analyses of several individual genes indicated putative regulatory properties of transcription termination events. Further studies are needed to find common denominators such as sequence motifs, secondary structures, or other signals that govern the choice of a specific RNA cleavage and transcription termination pathway. ",
author = "Ewa Molska",
note = "Udgivet: 02-03-2018",
year = "2018",
language = "English",

}

RIS

TY - BOOK

T1 - Global investigation of RNA 3'end processing and transcription termination pathways

T2 - termination pathways

AU - Molska, Ewa

N1 - Udgivet: 02-03-2018

PY - 2018

Y1 - 2018

N2 - RNA polymerases transcribe diverse classes of genes and the produced RNAs need to be targeted to their appropriate cognate biochemical maturation pathways. The vast majority of the human transcriptome consists of long non-coding RNAs (lncRNAs), which is a heterogeneous group of RNAs that is inadequately divided into classes based e.g. on length, stability and association with protein-coding genes. We reasoned that further classification based on biochemical properties, in this case transcription termination and the mechanistically coupled RNA 3’-end processing, would enable a better understanding about the biogenesis and possible functionality of such transcripts. Many lncRNAs are short-lived, which makes them difficult to detect with standard methods. Therefore, we applied a specialized next generation sequencing protocol called transient transcriptome sequencing (TT-seq) that allows the study of transcription termination on genes encoding both stable and unstable transcripts. We successfully obtained TT-seq data enriched for unstable lncRNAs from human cells depleted of factors known to be involved in transcription termination and RNA 3’-end processing. We developed a data-driven annotation protocol, which aided the discovery of transient RNA species and enabled determination of the pathways responsible for transcription termination on a multitude of genes. Our results demonstrate that genes corresponding to specific RNA classes do not pertain to one specific transcription termination pathway. For example, contrary to prediction, a subset of protein-coding genes utilise the machinery used by genes encoding U snRNAs. This same machinery is predominantly used by a class of lncRNA genes, encoding so-called PROMPTs, despite the presence of sequence elements predicted to guide the usage of the pathway mainly used by protein-coding genes. Thus, our results underscore the importance of functional studies over bioinformatic prediction. Analyses of several individual genes indicated putative regulatory properties of transcription termination events. Further studies are needed to find common denominators such as sequence motifs, secondary structures, or other signals that govern the choice of a specific RNA cleavage and transcription termination pathway.

AB - RNA polymerases transcribe diverse classes of genes and the produced RNAs need to be targeted to their appropriate cognate biochemical maturation pathways. The vast majority of the human transcriptome consists of long non-coding RNAs (lncRNAs), which is a heterogeneous group of RNAs that is inadequately divided into classes based e.g. on length, stability and association with protein-coding genes. We reasoned that further classification based on biochemical properties, in this case transcription termination and the mechanistically coupled RNA 3’-end processing, would enable a better understanding about the biogenesis and possible functionality of such transcripts. Many lncRNAs are short-lived, which makes them difficult to detect with standard methods. Therefore, we applied a specialized next generation sequencing protocol called transient transcriptome sequencing (TT-seq) that allows the study of transcription termination on genes encoding both stable and unstable transcripts. We successfully obtained TT-seq data enriched for unstable lncRNAs from human cells depleted of factors known to be involved in transcription termination and RNA 3’-end processing. We developed a data-driven annotation protocol, which aided the discovery of transient RNA species and enabled determination of the pathways responsible for transcription termination on a multitude of genes. Our results demonstrate that genes corresponding to specific RNA classes do not pertain to one specific transcription termination pathway. For example, contrary to prediction, a subset of protein-coding genes utilise the machinery used by genes encoding U snRNAs. This same machinery is predominantly used by a class of lncRNA genes, encoding so-called PROMPTs, despite the presence of sequence elements predicted to guide the usage of the pathway mainly used by protein-coding genes. Thus, our results underscore the importance of functional studies over bioinformatic prediction. Analyses of several individual genes indicated putative regulatory properties of transcription termination events. Further studies are needed to find common denominators such as sequence motifs, secondary structures, or other signals that govern the choice of a specific RNA cleavage and transcription termination pathway.

M3 - Ph.D. thesis

BT - Global investigation of RNA 3'end processing and transcription termination pathways

ER -