Epigenetics to proteomics: From yeast to brain

Bhargava, Poonam

doi:10.1002/pmic.200900464

Cited by 8 publications

(2 citation statements)

References 249 publications

(279 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Yeasts have been used as models for higher level complex organisms, including mammals and humans 40 . Whole-genome sequencing studies have shown that yeasts have similar genome size, gene content, and colinearity of genes along the chromosomes of species 41 .…”

Section: Introductionmentioning

confidence: 99%

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

Feng

Lin

Zhou

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, and limited types of evolutionary events. Here, we provide an alternative way to resolve phylogenetic problems based on analyses of real genome data. We use phylogenetic signals from all types of genome level evolutionary events, and overcome the conflicting issues existing in traditional phylogenetic approaches. Further, we build an automated computational pipeline to reconstruct phylogenies and ancestral genomes for two high-resolution real yeast genome datasets. Comparison results with recent studies and publications show that we reconstruct very accurate and robust phylogenies and ancestors. Finally, we identify and analyze the conserved syntenic blocks among reconstructed ancestral genomes and present yeast species.

show abstract

Section: Introductionmentioning

confidence: 99%

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

Feng

Lin

Zhou

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Proteomic approaches have been used as strong tools to find the global interacting partners of many complexes (24)(25)(26)(27). Therefore, in order to find the possible regulatory partners of the pol III TC, we followed AP-MS proteomic approaches (28) wherein we selected one subunit of each component to pull down the interacting partners in its transcriptionally active and repressed (nutrient starvation) states.…”

Section: Introductionmentioning

confidence: 99%

Yeast PAF1 complex restricts the accumulation of RNA polymerase III and counters the replication stress on the transcribed genes

Bhalla

Vernekar

Shukla

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Many regulatory proteins and complexes influence transcription by RNA polymerase (pol) II.In comparison, only a few regulatory proteins are known for pol III, which transcribes mostly house-keeping and non-coding genes. Yet, pol III transcription is precisely regulated under various stress conditions like starvation. We used pol III transcription complex components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits to identify potential interactors through mass spectrometry-based proteomics. A large interactome constituting known chromatin modifiers, factors and regulators of transcription by pol I and pol II revealed the possibility of a large number of signaling cues for pol III transcription against adverse conditions. We found one of the pol II-associated factors, Paf1 complex (PAF1C) interacts with the three baits. Its occupancy on the pol III-transcribed genes is low and not correlated with pol III occupancy. Paf1 deletion leads to higher occupancy of pol III, γ-H2A and DNA pol2 but no change in nucleosome positions. Genotoxins exposure causes pol III but not Paf1 loss from the genes. PAF1C promotes the pol III pausing and restricts its accumulation on the genes, which reduces the replication stress caused by the pol III barrier and transcriptionreplication conflict on these highly transcribed genes.

show abstract

Current awareness on yeast

2010

Yeast

View full text Add to dashboard Cite

In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on yeasts. Each bibliography is divided into 10 sections. 1 Reviews; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (5 weeks journals ‐ search completed 2nd. June 2010)

show abstract

Epigenetics to proteomics: From yeast to brain

Cited by 8 publications

References 249 publications

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

Yeast PAF1 complex restricts the accumulation of RNA polymerase III and counters the replication stress on the transcribed genes

Current awareness on yeast

Contact Info

Product

Resources

About