This document discusses how light regulates alternative splicing in plants through controlling transcription elongation. It presents a study that investigated the effects of light-dark conditions and histone deacetylase inhibitors on alternative splicing in Arabidopsis seedlings. The study found that light increases RNA polymerase II elongation, which regulates alternative splicing. Light-dark conditions affected alternative splicing but not total mRNA levels. The results suggest that kinetic coupling between transcription and alternative splicing is an important mechanism for plants to respond to environmental cues like light.
Gene silencing techniques for crop improvementJhilickBanerjee
Gene silencing is a technique that aims to reduce or eliminate the production of a protein from its corresponding gene. Gene silencing is the regulation of gene expression in a cell.
Gene silencing can occur during either transcription or translation.
Gene silencing is often considered as “Gene knockdown’ i.e their expression is reduced. In contrast , when genes are knocked out they are completely erased from the organism’s genome and thus have no expression.
Methods used to silence genes include RNAi, CRISPR or siRNA, these reduce the expression of the gene by 70% but do not completely eliminate it.
Gene silencing techniques for crop improvementJhilickBanerjee
Gene silencing is a technique that aims to reduce or eliminate the production of a protein from its corresponding gene. Gene silencing is the regulation of gene expression in a cell.
Gene silencing can occur during either transcription or translation.
Gene silencing is often considered as “Gene knockdown’ i.e their expression is reduced. In contrast , when genes are knocked out they are completely erased from the organism’s genome and thus have no expression.
Methods used to silence genes include RNAi, CRISPR or siRNA, these reduce the expression of the gene by 70% but do not completely eliminate it.
RNA interference [ RNAi] is a sequence mechanism , triggered by the introduction of ds RNA leading to mRNA degradation
It results in switching the targeted gene on and off at transcriptional or post transcriptional level3
The long double stranded RNAs enter a cellular pathway that is known as RNA interference pathway .
First ds RNAs get processed into 20-25 nucleotides small interfering RNAs [siRNAs] by an enzyme Dicer .
Small interfering RNAs assemble into RNA induced silencing complexes [RISCs] ,unwinding in the process.
The siRNAs strands subsequently guide the RISCs complementary RNA molecules , where they cleave and destroy the RNA .
Cleavage of RNA takes place near the middle of the region bound by siRNA strand .
This results into mRNA Degradation.
Gene knockdown
Double stranded RNA is synthesized with a sequence complementary to a gene of interest and introduced into a cell organism ,where it is recognized as exogenous genetic material and activates the RNAi pathway .
Using this mechanism, researchers can cause drastic decrease in the expresssion of targeted gene .
Since RNAi may not totally abolish expression of the gene , this technique is referred to as knockdown.
RNA interference [ RNAi] is a sequence mechanism , triggered by the introduction of ds RNA leading to mRNA degradation
It results in switching the targeted gene on and off at transcriptional or post transcriptional level3
The long double stranded RNAs enter a cellular pathway that is known as RNA interference pathway .
First ds RNAs get processed into 20-25 nucleotides small interfering RNAs [siRNAs] by an enzyme Dicer .
Small interfering RNAs assemble into RNA induced silencing complexes [RISCs] ,unwinding in the process.
The siRNAs strands subsequently guide the RISCs complementary RNA molecules , where they cleave and destroy the RNA .
Cleavage of RNA takes place near the middle of the region bound by siRNA strand .
This results into mRNA Degradation.
Gene knockdown
Double stranded RNA is synthesized with a sequence complementary to a gene of interest and introduced into a cell organism ,where it is recognized as exogenous genetic material and activates the RNAi pathway .
Using this mechanism, researchers can cause drastic decrease in the expresssion of targeted gene .
Since RNAi may not totally abolish expression of the gene , this technique is referred to as knockdown.
Molecular Systematics provides a solid conceptual basis for the evolutionary history of organisms. Molecular systematics is the study of DNA and RNA sequences to infer evolutionary links across organisms. Molecular approaches/ techniques provide excellent resources for the study of evolution and phylogeny.
"Introns: Structure and Functions" during November, 2011 (Friday Seminar activity, Department of Biotechnology, University of Agricultural Sciences, Dharwad, Karnataka) by Yogesh S Bhagat (Ph D Scholar)
COMPETENCY 3Integrate credible and relevant sources into coursewLynellBull52
COMPETENCY 3
Integrate credible and relevant sources into coursework to enhance clarity and support claims.
CRITERION
Reflect on how credibility and relevance of a chosen resource were determined.
Your result: Non-Performance
Distinguished
Reflects on how credibility and relevance of a chosen resource were determined. Notes how specific aspects of the assessment were used to determine relevance.
Proficient
Reflects on how credibility and relevance of a chosen resource were determined.
Basic
Explains the concepts of credibility and relevance in general terms, but does not specifically address how this was used to determine if the specific resource was credible and relevant.
Non-Performance
Does not explain the concepts of credibility and relevance in general terms.
Faculty Comments:
I did not see a discussion of source credibility/relevance. For this assignment you were are also required to locate an article in the library about time organizing strategies (outlined in Part I). Then, you were asked in Part II to reflect on how you determined the credibility and relevance of your chosen library resource to support your task prioritization.
ONCOLOGY LETTERS 19: 595-605, 2020
Abstract. Numerous types of molecular mechanisms mediate
the development of cancer. Non-coding RNAs (ncRNAs) are
being increasingly recognized to play important role in medi-
ating the development of diseases, including cancer. Long
non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are
the two most widely studied ncRNAs. Thus far, lncRNAs are
known to have biological roles through a variety of mecha-
nisms, including genetic imprinting, chromatin remodeling,
cell cycle control, splicing regulation, mRNA decay and
translational regulation, and miRNAs regulate gene expres-
sion through the degradation of mRNAs and lncRNAs.
Although ncRNAs account for a major proportion of the total
RNA, the mechanisms underlying the physiological or patho-
logical processes mediated by various types of ncRNAs, and
the specific interaction mechanisms between miRNAs and
lncRNAs in various physiological and pathological processes,
remain largely unknown. Thus, further research in this field
is required. In general, the interaction mechanisms between
miRNAs and lncRNAs in human cancer have become
important research topics, and the study thereof has led to
the recent development of related technologies. By providing
examples and descriptions, and performing chart analysis, the
present study aimed to review the interaction mechanisms and
research approaches for these two types of ncRNAs, as well
as their roles in the occurrence and development of cancer.
These details have far‑reaching significance for the utilization
of these molecules in the diagnosis and treatment of cancer.
Contents
1. Introduction
2. Interactions between lncRNAs and miRNAs
3. Methods of research in to lncRNAs and miRNAs
4. lncRNAs and miRNAs in cancer
5. Conclusion
1. Introduction
In 1993, Lee e ...
This is a presentation slide about cellular RNA interference process and RNA interference technology. Contains basic information about biology of cellular RNA interference processes and its discovery, and RNA interference technology. Also gives you the history and development of in-vitro and in-vivo technologies for applicability of RNA interference technology.
siRNA synthesis, siRNA libraries, siRNA delivering techniques, Electroporation, viral transfection methods, Advantages and disadvantages of RNA interference technology.
details about the preliminary and pre-clinical experiments of RNA interference as well as clinical trials of RNA interference.
Physico-chemical treatments to improve the functional properties and digesti...ShreyaMandal4
Starch is the main component which provides people with metabolic energy and nutrients. Retrogradation, syneresis, inability to sustain shear stress, and its unstable nature at different temperatures and pH environments limit the applicability of starch in its natural state. Therefore, to increase the economic value, modifications are needed to improve their physicochemical and functional properties. Various technologies, such as autoclaving-retrogradation, and complexation with other food-derived components such as protein, polyphenol, and hydrophobic antioxidant, have been used to reduce starch digestibility. Hydrothermal treatments, such as annealing and heat-moisture treatment, are also beneficial in modulating starch hierarchical structures and lowering RDS content. Various starch-related enzymes, such as α-amylases, β-amylases, transglucosidases, pullulanases, isoamylases have been widely used in the enzymatic approach to retard retrogradation and boost starch enzymatic resistance. The effects of gamma irradiation on the physico-chemical, thermal, functional, and microbiological properties of various flours have been studied by a number of researchers. Despite having a negative impact on the starch granules' crystallographic patterns, HMT was found to have a good impact on the nutritional (resistant starch) and functional aspects of the modified starches. Hence, Heat moisture treatment (HMT) in three cycles utilising an oven (OHMT) and autoclave (AHMT) (100°C and 120°C; moisture levels: 15%, 22%, and 30%) successfully improved the physical, chemical, and digestibility properties of purple yam flour. All of the treatments raised SDS (4–16%) and RS (7–13% and 5–18%), respectively, and altered the X-ray diffraction pattern and intensity. OHTM and AHMT both improved relative crystallinity by 6–19% and 10–20%, respectively. The treated purple yam flour can be used as a prebiotic carbohydrates source based on the findings. However, more research is needed into the optimal HMT temperature periods as well as their impact on the starch's other nutritional qualities.
Improvement in nutritional quality of spices through potential use of titan...ShreyaMandal4
Nutrient deficiency in food crops is seriously affecting human health, especially those in the rural areas. There are several ways of fortifying the nutrients in food such as dietary diversification, use of drugs and industrial fortification. One of the most intensively consumed metal oxide nanoparticles (NPs) worldwide, titanium dioxide nanoparticles (nTiO₂) is applied in many widely used products, such as in food production, in personal care products, in electronics and pharmaceuticals, and in environmental remediation. To date, little information is available on whether nTiO₂ amendment can enhance vegetable nutritional quality and alter spatial distribution of the important nutrient elements in the edible tissues. To address this knowledge gap, the vegetable coriander was selected as a model plant species. Coriander is an aromatic annual herb in Apiaceae family and possesses significant nutritional and medicinal properties. In this study, coriander (Coriandrum sativum L.) was treated with 0, 50, 100, 200, and 400 mg/L nTiO₂ to evaluate their possible benefit to plant growth and nutritional quality under hydroponic conditions. Observations showed that 50 mg/L nTiO₂ significantly increased the root and shoot fresh biomass by 13.2 % and 4.1 %, respectively, relative to the control. nTiO₂ at this level promoted shoot K, Ca, Mg, Fe, Mn, Zn, and B accumulation, while spatial distribution of K, Ca, Fe, Mn, Cu and Zn in coriander leaves was not affected. No nTiO₂ internalization or translocation to shoots occurred. 400 mg/L nTiO₂ significantly reduced root fresh biomass by 15.8 % and water content by 6.7%. Moreover, this high dose induced root cell membrane wrinkling, attributable to their aggregation and adsorption on root surfaces. At 100–400 mg/L concentration, antioxidant defense systems (SOD, CAT and APX) in plant were triggered to alleviate oxidative stress. At an appropriate dose (50 mg/L), nTiO₂ can improve nutrient quality of edible tissues without exerting toxicity to plant or posing health risk to consumers.
Understanding the role of the wrky gene family under stress in pigeonpeaShreyaMandal4
Pigeonpea (Cajanus cajan L.), a protein-rich legume, is a major food component of the daily diet for residents in semi-arid tropical regions of the word. WRKY, a large transcription factor gene family involved in numerous biological processes like seed germination, metabolism, plant growth, biotic and abiotic stress
responses was performed in pigeon pea. The study
will be helpful to understand the evolution, regulation, and distribution of the WRKY gene family, and additional exploration for the development of stress tolerance cultivars in pigeon pea and other legumes crops.
Cross the Best with the Best, and Select the Best: HELP in Breeding Selfing ...ShreyaMandal4
Hybrid-enabled line profiling (HELP) is a new
integrated breeding strategy for self-fertilizing crops that combines existing and recently identified elements, resulting in a strategy that synergistically exceeds existing breeding concepts.
Industrial fermentation-Does Fermentation Really Increase the Phenolic Conten...ShreyaMandal4
Decortication leads to a reduction in minerals, fibers, and antioxidants as phenolic compounds located in the peripheral parts of the grains. Fermentation can be applied to treat the whole nondecorticated flour to prevent functional loss. Bringing out the nutritional benefits of millets upon fermentation will serve us to include millets at a proportion in our meals along with traditional cereals.
Salt overly sensitive pathway constituting of SOS 3, SOS 2, SOS 1 has been reported to play significant fine tuning of Na+ ion extrusion and Na+ ion compartmentalization in plant cells, tissues.
¹³C Isotope Tracing to Delineate Altered Choline Metabolism in Proliferating ...ShreyaMandal4
Choline is conditionally essential nutrient for humans and many other animals. Choline is needed to produce acetylcholine, a neurotransmitter. Cancers usually exhibit a significantly altered choline phospholipid metabolite profile that is characterized by elevations of phosphatidylcholines and total choline containing compounds compared with those in normal tissues.
To Grow or Not to Grow: A long and winding sTORyShreyaMandal4
This slide presentation describes a brief discussion on Target of Rapamycin and its signalling. The results of network signalling determines the plants growth in adverse condition, orchestrate the survival mechanism beautifully.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
2. Presented by –
SHREYA MANDAL
Roll No: 21104 (M.Sc.)
Division of BIOCHEMISTRY
LIGHT REGULATES PLANT ALTERNATIVE
SPLICING THROUGH THE CONTROL OF
TRANSCRIPTION ELONGATION
3. INTRODUCTION
Light induces massive reprogramming of gene
expression in plants. Light is the most crucial external
signal perceived by plants.
Plants utilize complex photoreceptor signalling
networks to sense different light conditions and adjust
their development.
The sensory photoreceptors and retrograde signalling
pathways co-ordinately regulate AS of pre-mRNAs.
AS is a major post-transcriptional mechanism to
enhance the diversity of proteome in response to
environmental signals.
AS is important for photosynthesis, flowering, defense
response and circadian clock.
4. STUDY
1
1. To investigate a putative role of chromatin structure on the
regulation of AS by light –dark conditions , Arabidopsis seedlings
are treated with histone deacetylase inhibitor trichostatin A(TSA).
2. To challenge the effect of light on AS through the control of
RNA Pol II elongation.
3. To investigate if light –dark conditions affect Pol II densities
along the genes whose AS is regulated by the same cues, ChIP
7. HISTORY OF ALTERNATIVE SPLICING
• Gilbert first discovered the alternative splicing in
bacteriophage(adenovirus) in 1977.
• The thyroid hormone calcitonin is the prominent example
of alternative splicing in mammalian cell. The gene
encodes a protein known as CGRP(calcitonin gene
related peptides).
• Drosophila melanogaster gene called Dscam, which could
potentially have 38,016 splice variants.
10. MECHANISM OF ALTERNATIVE
SPLICING
o The decision of splice site selection involves RNA sequence
elements and trans acting factors such as:
Serine Arginine rich proteins
Heterogeneous nuclear ribonucleoproteins
o Depending on the position and function of the cis -regulatory
element, they are divided into following 4 groups:
Exonic splicing enhancers(ESEs)
Exonic splicing silencers(ESSs)
Intronic splicing enhancers(ISEs)
Intronic splicing silencers(ISSs)
11. SR PROTEIN
• 200- 600 amino acids in
length.
• In 1990, SR proteins
were discovered in
Drosophila.
• The RS domain
interacts with the
hyper-phosphorylated
CTD of the largest
subunit of RNA
polymerase II during
elongation of
transcription.
Domain configuration of human serine/arginine(SR)
proteins. Serine/arginine-rich splicing factor (SRSF) 1–12
are members of the SR protein splicing family that is
defined by the N-terminal RNA recognition motifs (RRMs)
followed by a downstream arginine/serine(RS) domain.
Source:WIREs RNA 2012, 3:1–12. doi: 10.1002/wrna.10O
12. Exon-dependent splicing activation by serine/arginine (SR) proteins. Exon bound SR proteins
interact with components of the general splicing machinery via RS domain interactions. SR
protein interactions with U2 snRNP auxiliary factor (U2AF) 35 (yellow) and U1 snRNP (blue) are
indicated to facilitate 3’splice site (U2AF) or 5’splice site (U1 snRNP) recognition. The splice
junctions are indicated by AG. and GU.
WIREs : RNA 2012, 3:1–12. doi:10.1002/wrna.100
13. HETEROGENEOUS NUCLEAR
RIBONUCLEOPROTEINS(hnRNPs)
• complexes of RNA and protein
• participate during gene transcription and subsequent post-
transcriptional modification of the newly synthesized RNA (pre-
mRNA).
• responsible for suppressing RNA splicing at a particular exon.
14. Exon-dependent splicing repression by heterogeneous nuclear
ribonucleoproteins(hnRNPs) proteins. Exon bound hnRNPs proteins
interfere with the association of the general splicing machinery with the
pre-mRNA. AG and GU indicate the splice junctions.
WIREs :RNA 2012,
3:112.
doi:10.1002/wrna.100
15. REGULATION BY TRANSCRIPTION COUPLING
THE RECRUITMENT MODEL:-
Different splicing factors
associate with the
transcription machinery
or the chromatin
template.
Increased concentration
of these factors in the
vicinity of the pre-mRNA,
regulate splicing choices
(Das et al.,2006).
THE KINETIC MODEL:-
The pace of transcription
elongation influences the
inclusion of alternative
exons.
Splicing machinery is
recruited sufficiently
quickly for spliceosome
assembly and splicing to
occur ( de la Mata et al.,
2003).
16. source: Journal of
RNA POL II KINETIC MODEL FOR AS
source: Lehninger Principles of Biochemistry, Fifth Edition
17. Epigenetic modifications of histones and/or DNA via methylation lead to altered
gene expression.
Yin and chung et al., (2011) Periodontal Disease – A Clinician’s guide
19. MATERIALS AND METHODS
Experimental Models:
o Arabidopsis Columbia ecotype (Col 0) was used as Wild –type.
o Mutant lines - a) hd1 mutant b) tfiis(Dolata et al.,2015)
Chemicals: a)Trichostatin A b) Camptothecin
Method : a. Radioactive RT-PCR b. q RT- PCR
c. Drug treatment d.Chromatin immuno-precipitation
e. Western blot
QUANTIFICATION AND STATISTICAL ANALYSIS :
o SMIT (Single Molecule Intron Tracking)
20. GROWTH CONDITIONS
Arabidopsis seeds were stratified for 3 days in the dark
germinated on MS medium containing 1% agar
seedlings were grown in Petri dishes (30 seeds per plate) with MS
medium at a const. temperature of 22°C under const. white light
provided by fluorescent with an intensity of irradiance between 70 and
100µmol/m² sec. for a period of 1-2 weeks.
transferred for 48 hour to darkness.
drug treatment, TSA or CPT and incubated in light or dark for additional
6 hr.
[ tfiis mutants were grown on soil for 3 weeks, incubated for 48 hr. in the
dark and then transferred to dark –light for 6 hr.]
24. CONCLUSION
Light controls Arabidopsis nuclear AS (Petrillo et
al).Light increases Pol II elongation while in darkness
elongation is lower.
Light regulation of AS is controlled by Pol II elongation.
The effect of light is abolished in a mutant plant
defective in Pol II elongation.
Changes in dark-light conditions affect AS, but not
total mRNA levels(overall transcription).
25. SUMMARY
AS regulation by transcription elongation is a mechanism to
respond to an environmental stimulus.
Kinetic coupling between transcription and AS is important for a
whole organism (plants) to respond to environmental cues(light).
More efforts will be needed to understand the mechanisms
involved in light mediated RNAPII elongation.
Nevertheless, this experimental system provides a mean to
investigate the mechanism behind the proposed regulation of AS by
transcription elongation in whole organisms..
26. Plants offer an advantage with respect with mammals to
investigate the importance of the kinetic coupling in a
whole organism in future advancements.
Future work from different groups will be needed in order
to decipher the precise nature of the mechanism
involved.