Alternative Splicing Regulation in Polypedilum vanderplanki Under Dehydration-rehydration Cycle
Investigation of genes involved in the processes of ensuring resistance to desiccation in Polypedilum vanderplanki. Comparison of survival, expression and splicing between knockdown and wild-type cells. Analysis of the dehydration-rehydration cycle.
| Рубрика | Медицина |
| Вид | дипломная работа |
| Язык | английский |
| Дата добавления | 17.08.2020 |
| Размер файла | 3,1 M |
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Supplementary
Table 6.1. Alignment summary
|
Sample |
Total number of reads |
Aligned exactly 1 time |
Aligned >1 times |
Overall alignment rate |
|
|
Pvd0_1 |
21774390 |
18347807 (84.26%) |
858284 (3.94%) |
88.20% |
|
|
Pvd0_2 |
12857477 |
11032865 (85.81%) |
486533 (3.78%) |
89.59% |
|
|
Pvd24_1 |
19396191 |
16308705 (84.08%) |
916509 (4.73%) |
88.81% |
|
|
Pvd24_2 |
16340821 |
13577380 (83.09%) |
679216 (4.16%) |
87.25% |
|
|
Pvd48_1 |
19023096 |
16262166 (85.49%) |
706860 (3.72%) |
89.20% |
|
|
Pvd48_2 |
20806541 |
17732728 (85.23%) |
713564 (3.43%) |
88.66% |
|
|
Pvr3_1 |
28028891 |
23984498 (85.57%) |
905135 (3.23%) |
88.80% |
|
|
Pvr3_2 |
14552083 |
12264687 (84.28%) |
456664 (3.14%) |
87.42% |
|
|
Pvr24_1 |
16162413 |
13702530 (84.78%) |
640241 (3.96%) |
88.74% |
|
|
Pvr24_2 |
16981094 |
14255599 (83.95%) |
799191 (4.71%) |
88.66% |
Table 6.2. The number of up- and down-expressed genes on different stages of the dehydration-rehydration cycle.
|
24 hours dehydration |
48 hours dehydration |
3 hours rehydration |
24 hours rehydration |
||
|
Down-regulated |
1974 (26%) |
2936 (38%) |
2737 (35%) |
1765 (22%) |
|
|
Up-regulated |
1704 (22%) |
2718 (35%) |
2632 (34%) |
1240 (16%) |
Table 6.3. Distribution of the datasets by the length of flanking introns.
|
EXN |
ALT |
down-regulated |
down-regulated d48 |
up-regulated |
up-regulated d48 |
||
|
upstream >= 200 & downstream >= 200 |
4043 / 10% |
1157 / 25% |
113 / 40% |
117 / 43% |
90 / 32% |
54 / 32% |
|
|
upstream >= 200 & downstream <= 200 |
7364 / 18% |
862 / 18% |
54 / 19% |
46 / 17% |
54 / 19% |
36 / 21% |
|
|
upstream <= 200 & downstream >= 200 |
5852 / 15% |
845 / 18% |
51 / 18% |
50 / 18% |
49 / 18% |
29 / 17% |
|
|
upstream <= 200 & downstream <= 200 |
22962 / 57% |
1836 / 39% |
63 / 23% |
59 / 22% |
88 / 31% |
52 / 30% |
Figure 6.1. Groups ratio of splicing segments in the dataset.
Table 6.4. Description of overrepresented motifs in test datasets.[53]
|
Motif name |
CISBP-RNA motif ID |
Intron location / test dataset vs control dataset |
RNA binding proteins |
Putative protein functions (flybase.org) |
|
|
bru-3 |
M117 |
Upstream down-regulated vs constant |
MSTRG.7874 |
RBP interacted with the EDEN element and mediates maternal mRNA translational repression |
|
|
orb2 |
M120 |
Upstream down-regulated vs constant |
MSTRG.614 |
Exhibits mRNA 3'-UTR binding activity; translation activator activity; and translation repressor activity, mRNA regulatory element binding. |
|
|
aret |
M003 M110 |
Upstream down-regulated vs constant |
MSTRG.10095 |
RBP acts in multiple forms of post-transcriptional gene regulation including repression and activation of translation and alternative splicing of pre-mRNAs. |
|
|
papi |
M011 |
Upstream & Downstream down-regulated vs constant |
MSTRG.4142 |
Exhibits protein N-terminus binding activity. Involved in negative regulation of transposon integration and positive regulation of cellular protein localization. |
|
|
elav |
M116 |
Upstream down-regulated vs constant |
MSTRG.4336 MSTRG.12277 MSTRG.9458 |
Exhibits poly(U) RNA binding activity. Involved in central nervous system development and negative regulation of mRNA 3'-end processing. |
|
|
fne |
M115 |
Upstream down-regulated vs constant |
RBP that works as a post-transcriptional regulator, exhibits poly(U) RNA binding activity. |
||
|
Rbp9 |
M124 |
Upstream down-regulated vs constant |
RBP involved in the establishment of the blood-brain barrier and control of germ cell proliferation. |
||
|
sm |
M067 |
Upstream down-regulated vs constant |
MSTRG.15360 |
RBP, heterogeneous nuclear ribonucleoprotein involved in axon guidance, mRNA processing, chemosensation. |
|
|
Pabp2 (Homo sapiens) |
M148_0.6 |
Downstream down-regulated vs constant |
MSTRG.6810 |
Exhibits poly(A) binding activity. Involved in mRNA polyadenylation; nuclear-transcribed mRNA poly(A) tail shortening; and positive regulation of protein glycosylation. |
|
|
tra2 |
M076 |
Upstream up-regulated vs alternative |
MSTRG.1051 |
RBP regulates the alternative splicing of several mRNAs including those from key regulators of sexual differentiation. |
Abbreviations
AS - alternative splicing
ALT - alternative segments, but not differentially spliced
BP or BS - branch splice site
BH - Benjamini-Hochberg correction
BLAST - Basic Local Alignment Search Tool
CREs - cis-regulatory element
DSCAM - Down syndrome cell adhesion molecule gene
ESEs - exonic splicing enhancers
ESSs - exonic splicing silencers
EXN - constitutive/constant segments
GO - gene ontology
hnRNP - heterogeneous nuclear ribonucleoproteins
HSF - heat shock factor
HSP - heat shock protein
ISEs - intronic splicing enhancers
ISSs - intronic splicing silencers
Ig - immunoglobulin
KH - K homology
LEA - Late Embryo Abundant
mRNA - messenger RNA
MDS - Multidimensional scaling plot
ncRNA - non-coding RNA
NMD - nonsense-mediated mRNA decay
PPT - polypyrimidine tract
PvD0 (d0) - samples of larvae in normal condition, before dehydration
PvD24 (d24) - samples after 24 hours of desiccation
PvD48 (d48) - samples after 48 hours of desiccation
PvR3 (r3) - samples after 3 hours of rehydration
PvR24 (r24) - samples after 24 hours of rehydration
PSI - inclusion ratio
PTCs - premature termination codons
PWM - position weight matrix
RNAPII - RNA polymerase II
RRM - RNA recognition motif
RGG - Arg-Gly-Gly tripeptides
RBP - RNA binding protein
snRNA - small nuclear RNA
snoRNA- small Nucleolar RNA
snRNP - small nuclear ribonucleoproteins
SS - splice site
SR - serine/arginine-rich protein
SF - splicing factor
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