Biology subjects

Gvozdenov, Z.

Publications and source records attributed to Gvozdenov, Z..

3 recordsLinked to original sources

bioRxiv2024

TRiC/CCT Chaperonin Governs RNA Polymerase II Activity in the Nucleus to Support RNA Homeostasis

The chaperonin TRiC/CCT is a large hetero-oligomeric ringed-structure that is essential in eukaryotes. While present in the nucleus, TRiC/CCT is typically considered to function in the cytosol where it mediates nascent polypeptide folding and the assembly/disassembly of protein complexes. Here, we investigated the nuclear role of TRiC/CCT. Inactivation of TRiC/CCT resulted in a significant increase in the production of nascent RNA leading to the accumulation of noncoding transcripts. The influence on transcription was not due to cytoplasmic TRiC/CCT-activities or other nuclear proteins as the effect was observed when TRiC/CCT was evicted from the nucleus and restricted to the cytoplasm. Rather, our data support a direct role of TRiC/CCT in regulating RNA polymerase II activity, as the chaperonin modulated nascent RNA production both in vivo and in vitro. Overall, our studies reveal a new avenue by which TRiC/CCT contributes to cell homeostasis by regulating the activity of nuclear RNA polymerase II.

molecular biology↗

bioRxiv2022

Genome-Wide Mapping of 5' Isoforms with 5'-Seq

Transcriptome of a genome is appreciated to be more complex than previously assumed. Same gene readouts can differ in terms of transcription start site, transcription end site and splicing. Growing evidence suggests functional importance of distinct transcript isoforms of the same gene. Obtaining these isoforms easily experimentally and processing data is crucial for prompt transcriptome functional characterizations. Here, I describe a quick protocol for generation of capped 5 isoforms sequencing library and 5 isoforms data analysis. The protocol relies on utilization of dephosphorylation-decapping method (oligo-capping), and it is a simplification of previously published 5 isoform studies. The pipeline for data analysis suggests several isoform features to focus on.

genomics↗

bioRxiv2022

High level and molecular nature of transcriptional noise in yeast cells

"Biological noise" is defined as functionally insignificant events that occur in living cells due to imperfect fidelity of biological processes. Distinguishing between biological function and biological noise is often difficult, and experiments to measure biological noise have not been performed. Here, we measure biological noise in yeast cells by analyzing chromatin structure and transcription of an 18 kb region of DNA whose sequence was randomly generated and hence lacks biological function. Nucleosome occupancy on random-sequence DNA is comparable to that on yeast genomic DNA. However, nucleosome-depleted regions are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of RNAs expressed from random-sequence DNA are comparable to those of typical yeast mRNAs, although transcription and mRNA decay rates are higher. Transcriptional initiation (5 ends) from random-sequence DNA occurs at numerous sites at low levels, indicating very low intrinsic specificity of the Pol II machinery. In contrast, poly(A) profiles (relative levels and clustering of 3 isoforms) of random-sequence RNAs are roughly comparable to those within 3 untranslated regions of yeast mRNAs, suggesting limited evolutionary constraints on poly(A) site choice. RNAs expressed from random-sequence DNA show higher cell-to-cell variability than RNAs expressed from yeast genomic DNA, suggesting that functional elements limit the variability among individual cells within a population. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.

molecular biology↗