Characterization of elements regulating gene transcription during regenerative neurogenesis:
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| 100 | 1 | |a Gourain, Victor Philippe Marie |d 1989- |e Verfasser |0 (DE-588)1219586765 |4 aut | |
| 245 | 1 | 0 | |a Characterization of elements regulating gene transcription during regenerative neurogenesis |c presented by M.Sc. and MSBI Victor Philippe Marie Gourain |
| 264 | 1 | |a Heidelberg |c [2020] | |
| 300 | |a 172 Seiten |b Illustrationen, Diagramme |c 30 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 502 | |b Dissertation |c Ruperto Carola University of Heidelberg, Germany |d 2020 | ||
| 546 | |a Text Englisch, Zusammenfassung in deutscher und englischer Sprache | ||
| 655 | 7 | |0 (DE-588)4113937-9 |a Hochschulschrift |2 gnd-content | |
| 856 | 4 | 2 | |m B:DE-101 |q application/pdf |u https://d-nb.info/1220363901/04 |3 Inhaltsverzeichnis |
| 856 | 4 | 2 | |m DNB Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032468005&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-032468005 | ||
Datensatz im Suchindex
| _version_ | 1804182055849820160 |
|---|---|
| adam_text | TABLE
OF
CONTENTS
ABBREVIATIONS
...............................................................................................................................................
8
PUBLICATIONS
.................................................................................................................................................
11
1.
INTRODUCTION
............................................................................................................................................
16
1.1
NEUROGENESIS
........................................................................................................................................
16
1.1.1
BRAIN
STRUCTURES
AND
CELLULAR
COMPONENTS
.......................................................................................
17
1.1.2
MOLECULAR
MECHANISMS
....................................................................................................................
21
1.1.3
REGENERATIVE
NEUROGENESIS
IN
ZEBRAFISH
.........................................................................................
22
1.2
ORGANIZATION
AND
TRANSCRIPTION
OF
GENES
..........................................................................................24
1.2.1
GENOME
ASSEMBLY
.............................................................................................................................
24
1.2.2
PRODUCTS
OF
GENE
TRANSCRIPTION
.........................................................................................................
24
1.3
REGULATION
OF
TRANSCRIPTION
..................................................................................................................
29
1.3.1
REGULATION
OF
TRANSCRIPTION
BY
TRANS-FACTORS
AND
C/S-ELEMENTS
......................................................
29
1.3.2
POST-TRANSCRIPTIONAL
REGULATION
OF
GENE
EXPRESSION
........................................................................
34
1.4
NEXT
GENERATION
SEQUENCING
AND
DATA
ANALYSIS
..................................................................................
37
1.4.1
NEXT
GENERATION
SEQUENCING
............................................................................................................
37
1.4.2
SEQUENCING
DATA
ANALYSIS..................................................................................................................
43
1.5
POSITION
OF
THE
PROJECT
AND
GOAL
..........................................................................................................45
1.5.1
REGULATION
OF
THE
TRANSCRIPTION
DURING
NEUROGENESIS
.....................................................................45
1.5.2
GOAL
...................................................................................................................................................47
2.
MATERIAL
AND
METHODS
...........................................................................................................................48
2.1
WET-LAB
.................................................................................................................................................48
2.1.1
FISH
COLLECTION
AND
CARE
....................................................................................................................
48
2.1.2
INJURY
AND
DISSECTION
OF
TELENCEPHALON,
AND
TOTAL
RNA
EXTRACTION
................................................
48
2.1.3
PREPARATION
OF
SEQUENCING
LIBRARIES
................................................................................................49
2.1.4
HIGH-THROUGHPUT
SEQUENCING
OF
LIBRARIES
........................................................................................
53
2.1.5
INVESTIGATIONS
OF
THE
SOXLB
C/S-REGULATORY
MODULE
CANDIDATE
.......................................................
57
2.2
DRY-LAB
...............................................................................................................................................
57
2.2.1
DEMULTIPLEXING
AND
QUALITY
CONTROL
OF
RAW
SEQUENCING
DATA
.........................................................
57
2.2.2
MAPPING
OF
SEQUENCING
READS
.........................................................................................................
60
2.2.3
ANALYSES
OF
THE
MRNASEQ
DATA
.......................................................................................................
61
2.2.4
ANALYSES
OF
SMALL
RNASEQ
DATA
.......................................................................................................
63
2.2.5
ANALYSIS
OF
CAGESEQ
DATA
.................................................................................................................
64
2.2.6
ANNOTATION
OF
SEQUENCING
RESULTS
...................................................................................................
67
5
2.2.7
IDENTIFICATION
OF
DISTAL
C/S-REGULATORY
MODULE
CANDIDATES
..............................................................
69
2.2.8
MULTI-SPECIES
COMPARISON
OF
GENOMIC
SEQUENCE
............................................................................
70
2.2.9
GRAPHICAL
REPRESENTATIONS
................................................................................................................
71
2.3
DEFINITIONS
............................................................................................................................................
71
2.4
SCRIPTS
...................................................................................................................................................
74
3
RESULTS
.....................................................................................................................................................
76
3.1
TRANSCRIPTS
AND
BIOLOGICAL
FUNCTIONS
OF
CORRESPONDING
GENES
IN
THE
ADULT
ZEBRAFISH
TELENCEPHALON
AFTER
INJURY
..................................................................................................................................................
76
3.1.1
VARIATIONS
IN
LEVELS
OF
TRANSCRIPTS
AFTER
INJURY
.................................................................................
76
3.1.2
BIOLOGICAL
FUNCTIONS
ENRICHED
AMONG
GENES
WITH
VARIATION
IN
LEVELS
OF
TRANSCRIPT
AFTER
INJURY....
77
3.1.3
LEVELS
OF
TRANSCRIPTS
CODING
FOR
ENZYMES
CATALYZING
CHOLESTEROL
SYNTHESIS
DECREASED
AFTER
INJURY
OF
THE
ADULT
ZEBRAFISH
TELENCEPHALON
.......................................................................................................
80
3.2
REGULATION
OF
TRANSCRIPTION
AFTER
INJURY
OF
THE
ADULT
ZEBRAFISH
TELENCEPHALON
..............................
84
3.2.1
ENRICHED
TRANSCRIPTION
FACTOR
BINDING
MOTIFS
IN
THE
PROMOTER
SEQUENCE
OF
GENES
WITH
VARIATION
IN
LEVELS
OF
TRANSCRIPT
AFTER
INJURY
.............................................................................................................
84
3.2.2
NON-CODING
GENES
CANDIDATES
WITH
A
POTIENTIAL
FUNCTION
IN
THE
REGULATION
OF
GENE
EXPRESSION
AFTER
INJURY
INFLICTED
TO
THE
ADULT
ZEBRAFISH
TELENCEPHALON
.....................................................................
88
3.2.2.1
CHARACTERIZATION
OF
NON-CODING
GENES
TRANSCRIBED
IN
THE
ADULT
ZEBRAFISH
TELENCEPHALON
......
88
3.2.2.2
LEVELS
OF
TRANSCRIPT
OF
95
NON-CODING
GENES
CHANGED
AFTER
INJURY
OF
THE
ADULT
ZEBRAFISH
TELENCEPHALON
............................................................................................................................................
95
3.2.3
DISTAL
C/S-REGULATORY
MODULE
CANDIDATES
TRANSCRIBED
IN
RESPONSE
TO
THE
INJURY
OF
ADULT
ZEBRAFISH
TELENCEPHALON
..........................................................................................................................................
100
3.2.3.1
INTERGENIC
ACTIVE
TRANSCRIPTION
START
SITES
INDICATING
THE
PRESENCE
OF
TRANSCRIBED
DISTAL
C/S-
REGULATORY
MODULE
CANDIDATES
...............................................................................................................
100
3.2.3.2
THE
SOXLB
DISTAL
C/S-REGULATORY
MODULE
CANDIDATE
TO
VALIDATE
THE
MODEL
OF
C/S-REGULATORY
MODULES
DISCOVERY
..................................................................................................................................
106
3.2.3.3
DISTAL
C/S-REGULATORY
MODULE
CANDIDATES
ACTIVATED
OR
REPRESSED
IN
RESPONSE
TO
ADULT
ZEBRAFISH
TELENCEPHALON
INJURY
...............................................................................................................................
112
3.3
POST-TRANSCRIPTIONAL
REGULATION
OF
PROTEIN-CODING
GENE
EXPRESSION
IN
RESPONSE
TO
ADULT
ZEBRAFISH
TELENCEPHALON
INJURY
................................................................................................................................
116
3.3.1
ALTERNATIVE
SPLICING
OF
RNAS
IN
RESPONSE
TO
ADULT
ZEBRAFISH
TELENCEPHALON
INJURY
.....................
116
3.3.2
VARIATION
IN
LEVELS
OF
MICRORNAS
IN
RESPONSE
TO
ADULT
ZEBRAFISH
TELENCEPHALON
INJURY
AND
PREDICTED
TARGET
PROTEIN-CODING
GENES
..................................................................................................
119
4.
DISCUSSION
..........................................................................................................................................
126
4.1
VARIATION
IN
LEVELS
OF
POLYADENYLATED
TRANSCRIPTS
AND
BIOLOGICAL
FUNCTIONS
OF
THE
CORRESPONDING
GENES
126
4.1.1
REGULATION
OF
THE
CHOLESTEROL
SYNTHESIS
AT
TRANSCRIPTIONAL
LEVEL
..................................................
126
6
4.1.2
MRNAS
CODING
FOR
TRANSPORTER
OF
CHOLESTEROL
AND
METABOLITES
...................................................
129
4.2
REGULATION
OF
TRANSCRIPTION
DURING
REGENERATIVE
NEUROGENESIS
....................................................
131
4.2.1
ROLE
OF
TRANSCRIPTION
FACTORS
...........................................................................................................
131
4.2.2
NON-CODING
RNAS
.............................................................................................................................
133
4.2.3
DISTAL
C/S-REGULATORY
MODULES
.........................................................................................................
133
4.3
POST-TRANSCRIPTIONAL
MODIFICATION
OF
GENE
EXPRESSION
...................................................................
138
4.4
CONCLUDING
REMARKS
AND
OUTLOOK
......................................................................................................
139
5.
ACKNOWLEDGMENTS
................................................................................................................................
141
6.
SUPPLEMENTARY
DATA
.............................................................................................................................
142
6.1
QUALITY
CONTROL
OF
SEQUENCING
DATA
...................................................................................................
142
6.2
NORMALIZATION
OF
TRANSCRIPT
LEVELS
.....................................................................................................
146
6.3
CONVERGENT
ANTISENSE
TRANSCRIPTION
..................................................................................................
150
7
LITERATURE
...............................................................................................................................................
152
7
|
| adam_txt |
TABLE
OF
CONTENTS
ABBREVIATIONS
.
8
PUBLICATIONS
.
11
1.
INTRODUCTION
.
16
1.1
NEUROGENESIS
.
16
1.1.1
BRAIN
STRUCTURES
AND
CELLULAR
COMPONENTS
.
17
1.1.2
MOLECULAR
MECHANISMS
.
21
1.1.3
REGENERATIVE
NEUROGENESIS
IN
ZEBRAFISH
.
22
1.2
ORGANIZATION
AND
TRANSCRIPTION
OF
GENES
.24
1.2.1
GENOME
ASSEMBLY
.
24
1.2.2
PRODUCTS
OF
GENE
TRANSCRIPTION
.
24
1.3
REGULATION
OF
TRANSCRIPTION
.
29
1.3.1
REGULATION
OF
TRANSCRIPTION
BY
TRANS-FACTORS
AND
C/S-ELEMENTS
.
29
1.3.2
POST-TRANSCRIPTIONAL
REGULATION
OF
GENE
EXPRESSION
.
34
1.4
NEXT
GENERATION
SEQUENCING
AND
DATA
ANALYSIS
.
37
1.4.1
NEXT
GENERATION
SEQUENCING
.
37
1.4.2
SEQUENCING
DATA
ANALYSIS.
43
1.5
POSITION
OF
THE
PROJECT
AND
GOAL
.45
1.5.1
REGULATION
OF
THE
TRANSCRIPTION
DURING
NEUROGENESIS
.45
1.5.2
GOAL
.47
2.
MATERIAL
AND
METHODS
.48
2.1
WET-LAB
.48
2.1.1
FISH
COLLECTION
AND
CARE
.
48
2.1.2
INJURY
AND
DISSECTION
OF
TELENCEPHALON,
AND
TOTAL
RNA
EXTRACTION
.
48
2.1.3
PREPARATION
OF
SEQUENCING
LIBRARIES
.49
2.1.4
HIGH-THROUGHPUT
SEQUENCING
OF
LIBRARIES
.
53
2.1.5
INVESTIGATIONS
OF
THE
SOXLB
C/S-REGULATORY
MODULE
CANDIDATE
.
57
2.2
DRY-LAB
.
57
2.2.1
DEMULTIPLEXING
AND
QUALITY
CONTROL
OF
RAW
SEQUENCING
DATA
.
57
2.2.2
MAPPING
OF
SEQUENCING
READS
.
60
2.2.3
ANALYSES
OF
THE
MRNASEQ
DATA
.
61
2.2.4
ANALYSES
OF
SMALL
RNASEQ
DATA
.
63
2.2.5
ANALYSIS
OF
CAGESEQ
DATA
.
64
2.2.6
ANNOTATION
OF
SEQUENCING
RESULTS
.
67
5
2.2.7
IDENTIFICATION
OF
DISTAL
C/S-REGULATORY
MODULE
CANDIDATES
.
69
2.2.8
MULTI-SPECIES
COMPARISON
OF
GENOMIC
SEQUENCE
.
70
2.2.9
GRAPHICAL
REPRESENTATIONS
.
71
2.3
DEFINITIONS
.
71
2.4
SCRIPTS
.
74
3
RESULTS
.
76
3.1
TRANSCRIPTS
AND
BIOLOGICAL
FUNCTIONS
OF
CORRESPONDING
GENES
IN
THE
ADULT
ZEBRAFISH
TELENCEPHALON
AFTER
INJURY
.
76
3.1.1
VARIATIONS
IN
LEVELS
OF
TRANSCRIPTS
AFTER
INJURY
.
76
3.1.2
BIOLOGICAL
FUNCTIONS
ENRICHED
AMONG
GENES
WITH
VARIATION
IN
LEVELS
OF
TRANSCRIPT
AFTER
INJURY.
77
3.1.3
LEVELS
OF
TRANSCRIPTS
CODING
FOR
ENZYMES
CATALYZING
CHOLESTEROL
SYNTHESIS
DECREASED
AFTER
INJURY
OF
THE
ADULT
ZEBRAFISH
TELENCEPHALON
.
80
3.2
REGULATION
OF
TRANSCRIPTION
AFTER
INJURY
OF
THE
ADULT
ZEBRAFISH
TELENCEPHALON
.
84
3.2.1
ENRICHED
TRANSCRIPTION
FACTOR
BINDING
MOTIFS
IN
THE
PROMOTER
SEQUENCE
OF
GENES
WITH
VARIATION
IN
LEVELS
OF
TRANSCRIPT
AFTER
INJURY
.
84
3.2.2
NON-CODING
GENES
CANDIDATES
WITH
A
POTIENTIAL
FUNCTION
IN
THE
REGULATION
OF
GENE
EXPRESSION
AFTER
INJURY
INFLICTED
TO
THE
ADULT
ZEBRAFISH
TELENCEPHALON
.
88
3.2.2.1
CHARACTERIZATION
OF
NON-CODING
GENES
TRANSCRIBED
IN
THE
ADULT
ZEBRAFISH
TELENCEPHALON
.
88
3.2.2.2
LEVELS
OF
TRANSCRIPT
OF
95
NON-CODING
GENES
CHANGED
AFTER
INJURY
OF
THE
ADULT
ZEBRAFISH
TELENCEPHALON
.
95
3.2.3
DISTAL
C/S-REGULATORY
MODULE
CANDIDATES
TRANSCRIBED
IN
RESPONSE
TO
THE
INJURY
OF
ADULT
ZEBRAFISH
TELENCEPHALON
.
100
3.2.3.1
INTERGENIC
ACTIVE
TRANSCRIPTION
START
SITES
INDICATING
THE
PRESENCE
OF
TRANSCRIBED
DISTAL
C/S-
REGULATORY
MODULE
CANDIDATES
.
100
3.2.3.2
THE
SOXLB
DISTAL
C/S-REGULATORY
MODULE
CANDIDATE
TO
VALIDATE
THE
MODEL
OF
C/S-REGULATORY
MODULES
DISCOVERY
.
106
3.2.3.3
DISTAL
C/S-REGULATORY
MODULE
CANDIDATES
ACTIVATED
OR
REPRESSED
IN
RESPONSE
TO
ADULT
ZEBRAFISH
TELENCEPHALON
INJURY
.
112
3.3
POST-TRANSCRIPTIONAL
REGULATION
OF
PROTEIN-CODING
GENE
EXPRESSION
IN
RESPONSE
TO
ADULT
ZEBRAFISH
TELENCEPHALON
INJURY
.
116
3.3.1
ALTERNATIVE
SPLICING
OF
RNAS
IN
RESPONSE
TO
ADULT
ZEBRAFISH
TELENCEPHALON
INJURY
.
116
3.3.2
VARIATION
IN
LEVELS
OF
MICRORNAS
IN
RESPONSE
TO
ADULT
ZEBRAFISH
TELENCEPHALON
INJURY
AND
PREDICTED
TARGET
PROTEIN-CODING
GENES
.
119
4.
DISCUSSION
.
126
4.1
VARIATION
IN
LEVELS
OF
POLYADENYLATED
TRANSCRIPTS
AND
BIOLOGICAL
FUNCTIONS
OF
THE
CORRESPONDING
GENES
126
4.1.1
REGULATION
OF
THE
CHOLESTEROL
SYNTHESIS
AT
TRANSCRIPTIONAL
LEVEL
.
126
6
4.1.2
MRNAS
CODING
FOR
TRANSPORTER
OF
CHOLESTEROL
AND
METABOLITES
.
129
4.2
REGULATION
OF
TRANSCRIPTION
DURING
REGENERATIVE
NEUROGENESIS
.
131
4.2.1
ROLE
OF
TRANSCRIPTION
FACTORS
.
131
4.2.2
NON-CODING
RNAS
.
133
4.2.3
DISTAL
C/S-REGULATORY
MODULES
.
133
4.3
POST-TRANSCRIPTIONAL
MODIFICATION
OF
GENE
EXPRESSION
.
138
4.4
CONCLUDING
REMARKS
AND
OUTLOOK
.
139
5.
ACKNOWLEDGMENTS
.
141
6.
SUPPLEMENTARY
DATA
.
142
6.1
QUALITY
CONTROL
OF
SEQUENCING
DATA
.
142
6.2
NORMALIZATION
OF
TRANSCRIPT
LEVELS
.
146
6.3
CONVERGENT
ANTISENSE
TRANSCRIPTION
.
150
7
LITERATURE
.
152
7 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author | Gourain, Victor Philippe Marie 1989- |
| author_GND | (DE-588)1219586765 |
| author_facet | Gourain, Victor Philippe Marie 1989- |
| author_role | aut |
| author_sort | Gourain, Victor Philippe Marie 1989- |
| author_variant | v p m g vpm vpmg |
| building | Verbundindex |
| bvnumber | BV047060837 |
| ctrlnum | (OCoLC)1225085927 (DE-599)KXP1735518360 |
| discipline | Biologie |
| discipline_str_mv | Biologie |
| format | Thesis Book |
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| genre | (DE-588)4113937-9 Hochschulschrift gnd-content |
| genre_facet | Hochschulschrift |
| id | DE-604.BV047060837 |
| illustrated | Illustrated |
| index_date | 2024-07-03T16:11:34Z |
| indexdate | 2024-07-10T09:01:28Z |
| institution | BVB |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-032468005 |
| oclc_num | 1225085927 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR |
| owner_facet | DE-355 DE-BY-UBR |
| physical | 172 Seiten Illustrationen, Diagramme 30 cm |
| publishDate | 2020 |
| publishDateSearch | 2020 |
| publishDateSort | 2020 |
| record_format | marc |
| spelling | Gourain, Victor Philippe Marie 1989- Verfasser (DE-588)1219586765 aut Characterization of elements regulating gene transcription during regenerative neurogenesis presented by M.Sc. and MSBI Victor Philippe Marie Gourain Heidelberg [2020] 172 Seiten Illustrationen, Diagramme 30 cm txt rdacontent n rdamedia nc rdacarrier Dissertation Ruperto Carola University of Heidelberg, Germany 2020 Text Englisch, Zusammenfassung in deutscher und englischer Sprache (DE-588)4113937-9 Hochschulschrift gnd-content B:DE-101 application/pdf https://d-nb.info/1220363901/04 Inhaltsverzeichnis DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032468005&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Gourain, Victor Philippe Marie 1989- Characterization of elements regulating gene transcription during regenerative neurogenesis |
| subject_GND | (DE-588)4113937-9 |
| title | Characterization of elements regulating gene transcription during regenerative neurogenesis |
| title_auth | Characterization of elements regulating gene transcription during regenerative neurogenesis |
| title_exact_search | Characterization of elements regulating gene transcription during regenerative neurogenesis |
| title_exact_search_txtP | Characterization of elements regulating gene transcription during regenerative neurogenesis |
| title_full | Characterization of elements regulating gene transcription during regenerative neurogenesis presented by M.Sc. and MSBI Victor Philippe Marie Gourain |
| title_fullStr | Characterization of elements regulating gene transcription during regenerative neurogenesis presented by M.Sc. and MSBI Victor Philippe Marie Gourain |
| title_full_unstemmed | Characterization of elements regulating gene transcription during regenerative neurogenesis presented by M.Sc. and MSBI Victor Philippe Marie Gourain |
| title_short | Characterization of elements regulating gene transcription during regenerative neurogenesis |
| title_sort | characterization of elements regulating gene transcription during regenerative neurogenesis |
| topic_facet | Hochschulschrift |
| url | https://d-nb.info/1220363901/04 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032468005&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT gourainvictorphilippemarie characterizationofelementsregulatinggenetranscriptionduringregenerativeneurogenesis |
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