25 papers · ranked by Valyu relevance
Lucy W. Barrett, Sue Fletcher, Steve D. Wilton
There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as “junk DNA”, it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal…
Silke Sperling
Considering that 80 genomes have been sequenced, providing us with the static information of the genome, it is still a long way to reveal the relationship between complex genotypes and phenotypes. The transcriptional regulation process is one of the obstacles that need to be understood to bridge our current information…
Elisa Buchberger, Micael Reis, Ting-Hsuan Lu, Nico Posnien
Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide…
Miriam Ruhinda, Roenick P. Olmo, Bianca C. Burini
Stability with Small Molecules: A Review of the ecDHFR Destabilizing Domain System Authors: Miriam Ruhinda, Roenick P. Olmo, Bianca C. Burini The E. coli dihydrofolate reductase (ecDHFR) destabilizing domain (DD) is a versatile post-translational tool for the conditional control of protein stability via ligand-induced…
Thomas Gross, Annette Becker
The flower of angiosperms is the most complex organ that plants generate and many transcription factors (TFs) are involved to regulate its morphogenesis in a coordinated way. In its center, the gynoecium develops consisting of specialized tissues such as secondary meristems, sites of postgenital fusion, ovules, pollen…
Alena Pance
Molecular biology is a rapidly evolving field that has led to the development of increasingly sophisticated technologies to improve our capacity to study cellular processes in much finer detail. Transcription is the first step in protein expression and the major point of regulation of the components that determine the…
Reza Rahmanzadeh
First, mutations leading to genetic novelties in a given species during evolution should be guided by the environment surrounding that species. Second, environment and germline are connected with each other via soma-germline messengers e.g., non-coding RNAs (ncRNAs). Third, based on the information that germline…
Olivia Angelin‐Bonnet, Patrick J. Biggs, Matthieu Vignes
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to familiarise the reader with the biological processes and molecular factors at play…
Vivian Tyng, Michael E. Kellman
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first show how linear models without feedback set the stage with a nonequilibrium steady…
J. M. Deutsch
Does regulation in the genome use collective behavior, similar to the way the brain or deep neural networks operate? Here I make the case for why having a genomic network capable of a high level of computation would be strongly selected for, and suggest how it might arise from biochemical processes that succeed in…
S.E. Romanov, D.A. Kalashnikova, P.P. Laktionov
for investigation of enhancers Методы высокопроизводительного репортерного анализа энхансеров Authors: ['S.E. Romanov' 'D.A. Kalashnikova' 'P.P. Laktionov'] The correct deployment of genetic programs for development and differentiation relies on finely coordinated regulation of specific gene sets. Genomic regulatory…
William T. Ireland, Suzannah M. Beeler, Emanuel Flores-Bautista, Nathan M. Belliveau + 4 more
'Nathan M. Belliveau' 'Michael J. Sweredoski' 'Annie Moradian' 'Justin B. Kinney' 'Rob Phillips'] Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli, for ≈ 65% of the promoters we remain completely ignorant of…
Dianbo Liu, Ryan Hannam, Luca Albergante
Differences in gene dosages between and within species are widely observed. Nevertheless, our understanding of the impacts of gene dosages on transcriptional regulation is far from complete and it is largely ignored in many genetic studies. In this article, we showed that dynamic properties of three genetic structures…
Laura Weinstock, Jenna Schambach, Anna Fisher, Cameron Kunstadt + 6 more
Understanding and controlling gene expression in organisms is essential for optimizing biological processes, whether in service of bioeconomic processes, human health, or environmental regulation. Epigenetic modifications play a significant role in regulating gene expression by altering chromatin structure, DNA…
Gat Krieger, Offir Lupo, Avraham A. Levy, Naama Barkai
Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells regulate gene expression to accommodate changing conditions. Previous comparative studies focused on specific conditions, describing inter-species variation in expression levels…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Nikoletta Psatha, Pavel Sova, Grigorios Georgolopoulos, Kiriaki Paschoudi + 12 more
Regulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors rely on the cellular and context specificity of regulatory DNA elements to express therapeutic transgenes…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Yue Wang, Siqi He
The expression of one gene might be regulated by its corresponding protein, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the existence of autoregulation with direct biochemical approaches.…
Benjamin Zoller, Shawn C. Little, Thomas Gregor
In early development, regulation of transcription results in precisely positioned and highly reproducible expression patterns that specify cellular identities. How transcription, a fundamentally noisy molecular process, is regulated to achieve reliable embryonic patterning remains unclear. In particular, it is unknown…
Mallory A. Laboulaye, Xin Duan, Mu Qiao, Irene E. Whitney + 1 more
Transgenic mouse lines are routinely employed to label and manipulate distinct cell types. The transgene generally comprises cell-type specific regulatory elements linked to a cDNA encoding a reporter or other proteins. However, off-target expression seemingly unrelated to the regulatory elements in the transgene is…
Rumiana Tenchov, Janet Sasso, Xinmei Wang, Qiongqiong Angela Zhou
Aging is a dynamic, time-dependent process characterized by a gradual accumulation of cell damage. Continual functional decline in the intrinsic ability of living organisms to accurately regulate homeostasis leads to increased susceptibility and vulnerability to diseases. Anti-aging research has a long history…
Authors not listed
Antisense oligonucleotides (ASOs) can modulate gene expression at the mRNA level, providing the ability to tackle conventionally undruggable targets and usher in an era of personalized medicine. A key mode of action for ASOs relies upon RNase H-engagement in the nucleus, however, the site for mature mRNA is the…
Authors not listed
In this report, we examine the extensive research landscape of CRISPR with an emphasis on CRISPR therapeutics and showcase our results from an in-depth analysis of the most up-to-date scientific information consisting of more than 53,000 publications encompassing academic journal articles and patents, spanning nearly…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…