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Elucidating the genetic and molecular basis of SWI/SNF-driven divergent non-coding transcription

Gowthaman, Uthra LU (2017) KBKM01 20171
Pure and Applied Biochemistry
Abstract
The discovery of pervasive transcription in eukaryotic organisms reveals that majority of promoters produce divergent non-coding transcripts besides their annotated transcripts. A recent study proposed the activation of divergent transcription by SWI/SNF chromatin remodelers. Mutating SNF5 subunit of the complex resulted in decreased levels of divergent transcription. Based on this finding, genomic replacement study was conducted. The yeast non-essential gene deletion library mutants were combined with snf5Δ. The screen aimed in identifying factors that suppress the snf5Δ and increase the levels of divergent non-coding transcription. SIN mutations in histones were reported to suppress the mutants of SWI/SNF complex. This hypothesis was... (More)
The discovery of pervasive transcription in eukaryotic organisms reveals that majority of promoters produce divergent non-coding transcripts besides their annotated transcripts. A recent study proposed the activation of divergent transcription by SWI/SNF chromatin remodelers. Mutating SNF5 subunit of the complex resulted in decreased levels of divergent transcription. Based on this finding, genomic replacement study was conducted. The yeast non-essential gene deletion library mutants were combined with snf5Δ. The screen aimed in identifying factors that suppress the snf5Δ and increase the levels of divergent non-coding transcription. SIN mutations in histones were reported to suppress the mutants of SWI/SNF complex. This hypothesis was tested by introducing snf5Δ into two SIN mutants from yeast histone mutant library. To monitor the transcripts, a bidirectional promoter construct was introduced into the mutants. The bidirectional promoter drives two fluorescent proteins in the coding and non-coding direction respectively. The fluorescence read-outs from high-throughput flow cytometry analysis showed estimates of coding and non-coding transcripts. Screening for suppressor factors from the non-essential gene deletion library resulted in 21 potential candidate factors. Re-transformation of two candidates SPT21 and HDA1 into snf5Δ background resulted in ratio of mCherry/YFP (coding/non-coding) signal weakly suppressing the effect of snf5Δ. However, a SIN mutant H4 V43 had less ratio of signal compared to snf5Δ testing positive for the hypothesis. (Less)
Please use this url to cite or link to this publication:
author
Gowthaman, Uthra LU
supervisor
organization
course
KBKM01 20171
year
type
H2 - Master's Degree (Two Years)
subject
keywords
eukaryotic organisms, SWI/SNF, transcripts, applied biochemistry
language
English
id
8908868
date added to LUP
2022-08-01 12:25:27
date last changed
2022-08-01 12:25:27
@misc{8908868,
  abstract     = {{The discovery of pervasive transcription in eukaryotic organisms reveals that majority of promoters produce divergent non-coding transcripts besides their annotated transcripts. A recent study proposed the activation of divergent transcription by SWI/SNF chromatin remodelers. Mutating SNF5 subunit of the complex resulted in decreased levels of divergent transcription. Based on this finding, genomic replacement study was conducted. The yeast non-essential gene deletion library mutants were combined with snf5Δ. The screen aimed in identifying factors that suppress the snf5Δ and increase the levels of divergent non-coding transcription. SIN mutations in histones were reported to suppress the mutants of SWI/SNF complex. This hypothesis was tested by introducing snf5Δ into two SIN mutants from yeast histone mutant library. To monitor the transcripts, a bidirectional promoter construct was introduced into the mutants. The bidirectional promoter drives two fluorescent proteins in the coding and non-coding direction respectively. The fluorescence read-outs from high-throughput flow cytometry analysis showed estimates of coding and non-coding transcripts. Screening for suppressor factors from the non-essential gene deletion library resulted in 21 potential candidate factors. Re-transformation of two candidates SPT21 and HDA1 into snf5Δ background resulted in ratio of mCherry/YFP (coding/non-coding) signal weakly suppressing the effect of snf5Δ. However, a SIN mutant H4 V43 had less ratio of signal compared to snf5Δ testing positive for the hypothesis.}},
  author       = {{Gowthaman, Uthra}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{Elucidating the genetic and molecular basis of SWI/SNF-driven divergent non-coding transcription}},
  year         = {{2017}},
}