Selection of new biological activities from random nucleotide sequences: evolutionary and practical considerations

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 112-117 ◽  
Author(s):  
Marshall S. Z. Horwitz ◽  
Dipak K. Dube ◽  
Lawrence A. Loeb
Keyword(s):  
Dna Sequences ◽  
Active Sites ◽  
Biological Activities ◽  
Regulatory Elements ◽  
Biologically Active ◽  
Protein Domain ◽  
Protein Coding ◽  
Coding Sequences ◽  
Future Success ◽  
Selection Of

Recent advances in the selection of biologically active DNA sequences from random populations are reviewed. Within the framework of evolution, forces are considered that have precluded the testing of all possible DNA sequences, purely with regard to their functionality as genetic regulatory elements or protein coding sequences. Examples are drawn from cassette mutagenesis of enzyme active sites, protein domain replacement by fusion with random genomic digests, and the selection of bacterial promoters from random DNA. Efforts to derive new activities are examined, and the likelihood of future success is evaluated.Key words: active DNA, nucleotide permutation, DNA evolution.

scholarly journals You're one in a googol: optimizing genes for protein expression

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Mark Welch ◽  
Alan Villalobos ◽  
Claes Gustafsson ◽  
Jeremy Minshull
Keyword(s):  
Protein Expression ◽  
Dna Sequences ◽  
Ad Hoc ◽  
Protein Coding ◽  
Vast Number ◽  
Coding Sequences ◽  
Affect Expression ◽  
Continue Work ◽  
Existing Data ◽  
Rational Sequence

A vast number of different nucleic acid sequences can all be translated by the genetic code into the same amino acid sequence. These sequences are not all equally useful however; the exact sequence chosen can have profound effects on the expression of the encoded protein. Despite the importance of protein-coding sequences, there has been little systematic study to identify parameters that affect expression. This is probably because protein expression has largely been tackled on an ad hoc basis in many independent projects: once a sequence has been obtained that yields adequate expression for that project, there is little incentive to continue work on the problem. Synthetic biology may now provide the impetus to transform protein expression folklore into design principles, so that DNA sequences may easily be designed to express any protein in any system. In this review, we offer a brief survey of the literature, outline the major challenges in interpreting existing data and constructing robust design algorithms, and propose a way to proceed towards the goal of rational sequence engineering.

A multiplexed miRNA and transgene expression platform for simultaneous repression and expression of protein coding sequences

2016 ◽  
Vol 12 (1) ◽  
pp. 295-312 ◽  
Author(s):  
Attila A. Seyhan
Keyword(s):  
Transgene Expression ◽  
Regulatory Elements ◽  
Protein Coding ◽  
Coding Sequences ◽  
Expression Platform ◽  
Simultaneous Delivery

A multiplexed intronic miRNA and transgene expression platform for simultaneous delivery of multiple negative (RNAi) and positive (transgene) regulatory elements.

scholarly journals Transcribed germline-limited coding sequences in Oxytricha trifallax

2020 ◽  
Author(s):  
Richard V. Miller ◽  
Rafik Neme ◽  
Derek M. Clay ◽  
Jananan S. Pathmanathan ◽  
Michael W. Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Rearrangement ◽  
Life Cycles ◽  
Open Reading Frames ◽  
Developmentally Regulated ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Dna Elimination ◽  
Nuclear Development

AbstractThe germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein coding sequences whose gene expression is terminated by DNA elimination.

scholarly journals HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations

2021 ◽  
Author(s):  
Naama Hirsch ◽  
Idit Dahan ◽  
Eva Dhaene ◽  
Matan Avni ◽  
Sarah Vergult ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Structural Variants ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Sequence ◽  
Shh Pathway ◽  
Essential Components ◽  
Ctcf Site

Structural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis-regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the Histone deacetylase 9 (HDAC9) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within HDAC9 sequence. Based on SVs within the HDAC9-TWIST1 locus, we defined the 3' HDAC9 sequence (~500Kb) as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7Δ/Δ) or Ctcf site (CtcfΔ/Δ) within the Hdac9 protein-coding sequence in mice led to decreased Twist1 expression and altered anterior\posterior limb expression patterns of Shh pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1+/− mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter region interacts with Hdac9 sequences that encompass Twist1 enhancers and a Ctcf site and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence (Hdac9INV/+) in mice that does not disrupt Hdac9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidated essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence, suggesting that SVs, encompassing protein-coding sequence, such as HDAC9, could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene, such as TWIST1.

scholarly journals The Biological Activities of Vitamin D and Its Receptor in Relation to Calcium and Bone Homeostasis, Cancer, Immune and Cardiovascular Systems, Skin Biology, and Oral Health

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
R. A. G. Khammissa ◽  
J. Fourie ◽  
M. H. Motswaledi ◽  
R. Ballyram ◽  
J. Lemmer ◽  
...  
Keyword(s):  
Vitamin D ◽  
Calcium Homeostasis ◽  
Dna Sequences ◽  
Target Genes ◽  
Biological Activities ◽  
Biological Effects ◽  
Active Form ◽  
Vitamin D Supplementation ◽  
Biologically Active ◽  
Bone Homeostasis

Vitamin D plays an important role in calcium homeostasis and bone metabolism, with the capacity to modulate innate and adaptive immune function, cardiovascular function, and proliferation and differentiation of both normal and malignant keratinocytes. 1,25(OH)2D, the biologically active form of vitamin D, exerts most of its functions through the almost universally distributed nuclear vitamin D receptor (VDR). Upon stimulation by 1,25(OH)2D, VDR forms a heterodimer with the retinoid X receptor (RXR). In turn, VDR/RXR binds to DNA sequences termed vitamin D response elements in target genes, regulating gene transcription. In order to exert its biological effects, VDR signalling interacts with other intracellular signalling pathways. In some cases 1,25(OH)2D exerts its biological effects without regulating either gene expression or protein synthesis. Although the regulatory role of vitamin D in many biological processes is well documented, there is not enough evidence to support the therapeutic use of vitamin D supplementation in the prevention or treatment of infectious, immunoinflammatory, or hyperproliferative disorders. In this review we highlight the effects of 1,25(OH)2D on bone and calcium homeostasis, on cancer, and refer to its effects on the cardiovascular and immune systems.

scholarly journals Complex Analysis of Retroposed Genes’ Contribution to Human Genome, Proteome and Transcriptome

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 542
Author(s):  
Magdalena Regina Kubiak ◽  
Michał Wojciech Szcześniak ◽  
Izabela Makałowska
Keyword(s):  
Complex Analysis ◽  
Genomic Sequence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Protein Domain ◽  
Gene Duplications ◽  
Protein Coding ◽  
Spatio Temporal ◽  
Recombination Hot Spots ◽  
Cis And Trans

Gene duplication is a major driver of organismal evolution. One of the main mechanisms of gene duplications is retroposition, a process in which mRNA is first transcribed into DNA and then reintegrated into the genome. Most gene retrocopies are depleted of the regulatory regions. Nevertheless, examples of functional retrogenes are rapidly increasing. These functions come from the gain of new spatio-temporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA and/or by selectively advantageous mutations, which may lead to the switch from protein coding to regulatory RNA. As recent studies have shown, these genes may lead to new protein domain formation through fusion with other genes, new regulatory RNAs or other regulatory elements. We utilized existing data from high-throughput technologies to create a complex description of retrogenes functionality. Our analysis led to the identification of human retroposed genes that substantially contributed to transcriptome and proteome. These retrocopies demonstrated the potential to encode proteins or short peptides, act as cis- and trans- Natural Antisense Transcripts (NATs), regulate their progenitors’ expression by competing for the same microRNAs, and provide a sequence to lncRNA and novel exons to existing protein-coding genes. Our study also revealed that retrocopies, similarly to retrotransposons, may act as recombination hot spots. To our best knowledge this is the first complex analysis of these functions of retrocopies.

scholarly journals Transcribed germline-limited coding sequences in Oxytricha trifallax

2021 ◽  
Author(s):  
Richard V Miller ◽  
Rafik Neme ◽  
Derek M Clay ◽  
Jananan S Pathmanathan ◽  
Michael W Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Rearrangement ◽  
Life Cycles ◽  
Open Reading Frames ◽  
Developmentally Regulated ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Dna Elimination ◽  
Nuclear Development

Abstract The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein-coding sequences whose gene expression is terminated by DNA elimination.

Genome organisation in the murine sperm nucleus

Zygote ◽  
1995 ◽  
Vol 3 (2) ◽  
pp. 123-131 ◽  
Author(s):  
Carol Jennings ◽  
Don Powell
Keyword(s):  
Repetitive Dna ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sperm Nucleus ◽  
Genome Organisation ◽  
Telomeric Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Restricted Domains

SummaryThe organisation of DNA sequences in the murine sperm nucleus was studied using in situ hybridisation of biotinylated DNA probes. The efficiency of this reaction was assessed using a dispersed repetitive DNA probe. Telomeric DNA was distributed around the nucleus. Centromeric and ribosomal DNA sequences occupied restricted domains in the sperm nucleus. DNA sequences for a transgene and a cluster of homeogenes occupied different, and rather less defined, domains. Together these results imply that both repetitive and protein-coding sequences are arranged in the nucleus in an ordered fashion.

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