The dynamic RNA-binding behavior of SR proteins
In the cell, the genetic information encoded in the DNA is transcribed to RNA. All RNAs that are transcribed in the cell are initially produced as precursor RNAs, which have to undergo various steps of processing to obtain their mature form. The maturation and processing for all RNA classes requires...
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Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden
2016
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Online Access: | http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-191373 http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-191373 http://www.qucosa.de/fileadmin/data/qucosa/documents/19137/Thesis-PhD-Brugiolo-Mattia-Final.pdf |
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ndltd-DRESDEN-oai-qucosa.de-bsz-14-qucosa-1913732016-01-12T03:30:38Z The dynamic RNA-binding behavior of SR proteins Brugiolo, Mattia RNA iCLIP SRSF3 SRSF7 RNA-binding iCLIP SRSF3 SRSF7 ddc:570 rvk:WD 5355 In the cell, the genetic information encoded in the DNA is transcribed to RNA. All RNAs that are transcribed in the cell are initially produced as precursor RNAs, which have to undergo various steps of processing to obtain their mature form. The maturation and processing for all RNA classes requires the activity of multiple RNA binding proteins (RBPs). An important family of RBPs that is involved in RNA maturation and processing is the SR-protein family. SR proteins are important for the regulation of a multitude of processes that include: splicing, transcription, export, RNA stabilization, translation and ncRNA processing. As of yet, there have been no comprehensive studies that describe how SR proteins dynamically regulate the maturation of RNAs. The results presented in this thesis provide new insights into the function and activity of SR proteins during RNA maturation. My experiments greatly expand the knowledge surrounding the action of RNA-binding proteins in vivo and in different cell compartments. To study the action of two different SR proteins in different cell compartments, I developed a new technique that combines cell fractionation and iCLIP, which I named FRACKING. For the first time, this method allowed me to collect information regarding the subcellular location where the RNA-protein interactions are taking place, giving a dynamic picture of the in vivo binding of SR proteins and of RNA binding proteins (RBP) in general. By using FRACKING on two heavily shuttling SR proteins, SRSF3 and SRSF7, I showed that both SR proteins are very dynamic in their binding behavior with RNAs. My research showed that both SRSF3 and SRSF7 strongly associate with RNAs during transcription (co-transcriptionally) and that they often remain bound to these transcripts until they are exported to the cytoplasm. The functions of SRSF3 and SRSF7 are closely related to their binding location on the target RNAs. I identified a subset of highly conserved introns that associated with SR proteins and are retained in their transcripts. These intron-retaining isoforms, contrary to textbook knowledge, are exported to the cytoplasm. I showed, for the first time, that SRSF3 and SRSF7 strongly interact with snoRNAs in the chromatin, and that this snoRNA-SR-protein binding behavior is distinct between SRSF3 and SRSF7. SRSF3 binds to the mature snoRNA sequence, and also to the surrounding intronic sequences, pointing towards a possible activity in guiding snoRNA maturation. Whereas SRSF7 associates to mature snoRNA sequences. Taken together, my study identified a dynamic pool of interactions for two SR proteins, in different cell compartments and discovered new activities for the two SR proteins. Importantly, this study challenges textbook knowledge on splicing and export of mRNAs by identifying a subset of transcripts that can be exported even when they retain introns. Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden Technische Universität Dresden, Fakultät Mathematik und Naturwissenschaften Prof. Dr. Karla Neugebauer Prof. Dr. Francis Stewart Prof. Dr. Karla Neugebauer 2016-01-11 doc-type:doctoralThesis application/pdf http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-191373 urn:nbn:de:bsz:14-qucosa-191373 http://www.qucosa.de/fileadmin/data/qucosa/documents/19137/Thesis-PhD-Brugiolo-Mattia-Final.pdf eng |
collection |
NDLTD |
language |
English |
format |
Doctoral Thesis |
sources |
NDLTD |
topic |
RNA iCLIP SRSF3 SRSF7 RNA-binding iCLIP SRSF3 SRSF7 ddc:570 rvk:WD 5355 |
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RNA iCLIP SRSF3 SRSF7 RNA-binding iCLIP SRSF3 SRSF7 ddc:570 rvk:WD 5355 Brugiolo, Mattia The dynamic RNA-binding behavior of SR proteins |
description |
In the cell, the genetic information encoded in the DNA is transcribed to RNA. All RNAs that are transcribed in the cell are initially produced as precursor RNAs, which have to undergo various steps of processing to obtain their mature form. The maturation and processing for all RNA classes requires the activity of multiple RNA binding proteins (RBPs). An important family of RBPs that is involved in RNA maturation and processing is the SR-protein family.
SR proteins are important for the regulation of a multitude of processes that include: splicing, transcription, export, RNA stabilization, translation and ncRNA processing. As of yet, there have been no comprehensive studies that describe how SR proteins dynamically regulate the maturation of RNAs.
The results presented in this thesis provide new insights into the function and activity of SR proteins during RNA maturation. My experiments greatly expand the knowledge surrounding the action of RNA-binding proteins in vivo and in different cell compartments.
To study the action of two different SR proteins in different cell compartments, I developed a new technique that combines cell fractionation and iCLIP, which I named FRACKING. For the first time, this method allowed me to collect information regarding the subcellular location where the RNA-protein interactions are taking place, giving a dynamic picture of the in vivo binding of SR proteins and of RNA binding proteins (RBP) in general.
By using FRACKING on two heavily shuttling SR proteins, SRSF3 and SRSF7, I showed that both SR proteins are very dynamic in their binding behavior with RNAs. My research showed that both SRSF3 and SRSF7 strongly associate with RNAs during transcription (co-transcriptionally) and that they often remain bound to these transcripts until they are exported to the cytoplasm. The functions of SRSF3 and SRSF7 are closely related to their binding location on the target RNAs. I identified a subset of highly conserved introns that associated with SR proteins and are retained in their transcripts. These intron-retaining isoforms, contrary to textbook knowledge, are exported to the cytoplasm.
I showed, for the first time, that SRSF3 and SRSF7 strongly interact with snoRNAs in the chromatin, and that this snoRNA-SR-protein binding behavior is distinct between SRSF3 and SRSF7. SRSF3 binds to the mature snoRNA sequence, and also to the surrounding intronic sequences, pointing towards a possible activity in guiding snoRNA maturation. Whereas SRSF7 associates to mature snoRNA sequences.
Taken together, my study identified a dynamic pool of interactions for two SR proteins, in different cell compartments and discovered new activities for the two SR proteins. Importantly, this study challenges textbook knowledge on splicing and export of mRNAs by identifying a subset of transcripts that can be exported even when they retain introns. |
author2 |
Technische Universität Dresden, Fakultät Mathematik und Naturwissenschaften |
author_facet |
Technische Universität Dresden, Fakultät Mathematik und Naturwissenschaften Brugiolo, Mattia |
author |
Brugiolo, Mattia |
author_sort |
Brugiolo, Mattia |
title |
The dynamic RNA-binding behavior of SR proteins |
title_short |
The dynamic RNA-binding behavior of SR proteins |
title_full |
The dynamic RNA-binding behavior of SR proteins |
title_fullStr |
The dynamic RNA-binding behavior of SR proteins |
title_full_unstemmed |
The dynamic RNA-binding behavior of SR proteins |
title_sort |
dynamic rna-binding behavior of sr proteins |
publisher |
Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden |
publishDate |
2016 |
url |
http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-191373 http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-191373 http://www.qucosa.de/fileadmin/data/qucosa/documents/19137/Thesis-PhD-Brugiolo-Mattia-Final.pdf |
work_keys_str_mv |
AT brugiolomattia thedynamicrnabindingbehaviorofsrproteins AT brugiolomattia dynamicrnabindingbehaviorofsrproteins |
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1718160363725258752 |