Workshop on Molecular Evolution

Workshop on Molecular Evolution: "Workshop on Molecular Evolution"

MIT OpenCourseWare | Health Sciences and Technology | HST.508 Quantitative Genomics,

MIT OpenCourseWare | Health Sciences and Technology | HST.508 Quantitative Genomics, Fall 2005 | Home: "HST.508 Quantitative Genomics"

diversity of Pcdh genes among teleosts

• In mammals, the protocadherins are encoded by three closely-linked clusters (α, β and γ) of tandem genes and are hypothesized to provide a molecular code for specifying the remarkably-diverse neural connections in the central nervous system.
• Like mammals, the coelacanth, a lobe-finned fish, contains a single protocadherin locus, also arranged into α, β and γ clusters.
• Zebrafish, however, possesses two protocadherin loci that contain more than twice the number of genes as the coelacanth, but arranged only into α and γ clusters.
• Fugu contains two unlinked protocadherin loci, Pcdh1 and Pcdh2, that collectively consist of at least 77 genes. The fugu Pcdh1 locus has been subject to extensive degeneration, resulting in the complete loss of Pcdh1γ cluster.The fugu Pcdh genes have undergone lineage-specific regional gene conversion processes that have resulted in a remarkable regional sequence homogenization among paralogs in the same subcluster.
• Besides the 'fish-specific' whole genome duplication, the evolution of protocadherin genes in teleost fishes is influenced by lineage-specific gene losses, tandem gene duplications and regional sequence homogenization.

Comparison of the fugu (FrPcdh1 and FrPcdh2), zebrafish (DrPcdh1 and DrPcdh2)and coelacanth (LmPcdh) protocadherin clusters. Variable exons in each paralog group are shown in different colors. Orthologs between fugu and zebrafish as well as the inter-locus paralogs between the two Pcdh loci in fugu or zebrafish are shown in the same colors. 'Teleost Pcdh1' and 'Teleost Pcdh2' are the Pcdh clusters predicted in the common ancestor of fugu and zebrafish, and 'Fish Pcdh ancestor' is the single Pcdh cluster predicted in the ray-finned fish prior to the 'fish-specific' whole genome duplication. The corresponding exons in the 'Fish Pcdh ancestor' and the inter-locus paralogs between 'Teleost Pcdh1' and 'Teleost Pcdh2' are shown in the same color except the 'αIV', which represents a common ancestor for fugu FrPcdh2α8–25 and zebrafish DrPcdh2α8–25. Among the exons predicted in the 'Fish Pcdh ancestor', those present in the Pcdh loci of both fugu and zebrafish are labeled with an asterisk.

a -22k CNE Controls Ifng Gene Expression by T Cells and NK Cells

"Chromatin dynamics that regulate Ifng gene expression are incompletely understood. By using cross-species comparative sequence analyses, we have identified conserved noncoding sequences (CNSs) upstream of the Ifng gene, one of which, located −22 kb from the transcriptional start site, contains clustered consensus binding sequences of transcription factors that function in T cell differentiation. CNS−22 was uniquely associated with histone modifications typical of accessible chromatin in both T helper 1 (Th1) and Th2 cells and demonstrated significant and selective T-bet (T-box transcription factor expressed in T cells, Tbx21)-dependent binding and enhancer activity in Th1 cells. Deletion of CNS−22 in the context of an Ifng reporter transgene ablated T cell receptor-dependent and -independent Ifng expression in Th1 effectors and similarly blocked expression by cytotoxic T lymphocytes and natural killer cells. Thus, a single distal element may be essential for Ifng gene expression by both innate and adaptive immune effector cell lineages."

Molecular biology: RNA in control

Cheah et al.[Nature] show that expression of the NMT1 gene is regulated at the level of pre-mRNA alternative splicing by a riboswitch that binds to thiamine pyrophosphate (TPP). a, At low concentrations of TPP, the TPP-binding (aptamer) region of the riboswitch base-pairs with sequences surrounding a splice site (red blocking line) in a nearby non-coding sequence, and prevents its selection by the splicing machinery. A distal splice site (green arrow) is selected, however, resulting in the generation of a shorter NMT1 mRNA with a coding sequence, or open reading frame (ORF), that translates into a functional NMT1-encoded protein (green signal). b, At high TPP levels, the aptamer undergoes a conformational rearrangement so that the region that was previously bound to the nearby splice site is now used to bind to TPP. This and other conformational changes (not shown) generate a longer mRNA splice variant that contains short, 'decoy' ORFs (red signal), preventing functional NMT1 expression.

Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster

"We describe here the Drosophila gene hydra that appears to have originated de novo in the melanogaster subgroup and subsequently evolved in both structure and expression level in Drosophila melanogaster and its sibling species. D. melanogasterhydra encodes a predicted protein of ~300 amino acids with no apparent similarity to any previously known proteins. The syntenic region flanking hydra on both sides is found in both D. ananassae and D. pseudoobscura, but hydra is found only in melanogaster subgroup species, suggesting that it originated less than ~13 million years ago. Exon 1 of hydra has undergone recurrent duplications, leading to the formation of nine tandem alternative exon 1s in D. melanogaster. Seven of these alternative exons are flanked on their 3' side by the transposon DINE-1 (Drosophila Interspersed Element-1). We demonstrate that at least four of the nine duplicated exon 1s can function as alternative transcription start sites. The entire hydra locus has also duplicated in D. simulans and D. sechellia. D. melanogasterhydra is expressed most intensely in the proximal testis, suggesting a role in late-stage spermatogenesis. The coding region of hydra has a relatively high Ka/Ks ratio between species but the ratio is less than one in all comparisons, suggesting that hydra is subject to functional constraint. Analysis of sequence polymorphism and divergence of hydra shows that it has evolved under positive selection in the lineage leading to D. melanogaster. The dramatic structural changes surrounding the first exons do not affect the tissue specificity of gene expression: hydra is expressed predominantly in the testes in D. melanogaster, D. simulans and D. yakuba. However, we have found that expression level changed dramatically (~>20 fold) between D. melanogaster and D. simulans. While hydra initially evolved in the absence of nearby transposable element insertions, we suggest that the subsequent accumulation of repetitive sequences in the hydra region may have contributed to structural and expression-level evolution by inducing rearrangements and causing local heterochromatinization. Our analysis further shows that recurrent evolution of both gene structure and expression level may be characteristics of newly evolved genes. We also suggest that late-stage spermatogenesis is the functional target for newly evolved and rapidly evolving male-specific genes."

use transition/transversion (κ) ratio test to detect functional polypeptide

"To confirm our results using an independent nucleotide-based approach (as opposed to the codon-based test described earlier), we applied the transition/transversion (κ) ratio test to make inferences about biological significance of ARFs. The test is based on the following reasoning: in most standard protein-coding regions (with only one reading frame), κ at the third codon position (κ3) is significantly different (higher) than at the first and second codon positions (κ12), so that κ12 < κ3 [15]. This is because most substitutions at the third codon position are synonymous, whereas in the first codon position all but eight substitutions are nonsynonymous, and all substitutions in the second codon position are nonsynonymous. By contrast, in overlapping reading frames, codon positions are codependent. For example, in a +1 ARF, the third codon positions correspond to the first codon positions of the canonical frame. Thus, almost every change in the third codon position of the ARF is guaranteed to change amino acids encoded in the canonical frame. However, if the ARF encodes a truly functional product, purifying selection would resist such changes, and the condition κ12 < κ3 would not hold. This gives us the opportunity to test functionality of ARF in our dataset by contrasting two hypotheses: H₀: κ₁₂ = κ₃ (ARF does encode functional polypeptide) and H_A: κ₁₂ < κ₃ (ARF does not encode functional polypeptide). To perform this test, we used a maximum likelihood framework to test κ₁₂ and κ₃ for equality [16]. Application of the test to our list of dual-coding genes identified 18 candidates" PLoS Computational Biology - A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes

300bp intronic regulatory element in hand gene

"Herein we describe the identification of a regulatory region in the hand gene essential and sufficient for the expression in the visceral mesoderm during embryogenesis. We found that hand expression in the circular visceral mesoderm is abolished in embryos mutant for the FoxF domain containing transcription factor Biniou. Furthermore we demonstrate that Biniou regulates hand expression by direct binding to a 300 bp sequence element, located within the 3rd intron of the hand gene. This regulatory element is highly conserved in different Drosophila species. In addition, we provide evidence that Hand is dispensable for the initial differentiation of the embryonic visceral mesoderm." (Hand is a direct target of the forkhead transcription factor Biniou during Drosophila visceral mesoderm differentiation.)

Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genom

"Analysis of 145 intergenic microRNA and all protein coding genes revealed that the upstream sequences of the former are up to twice as conserved as the latter amongst mammals, except in the first 500 bp where the conservation is similar. Comparison of the promoter conservation in 513 protein coding genes and related transcription factor binding sites (TFBSs) showed that 41% of the known human TFBSs are located in the 6.7% of promoter regions that are human-opossum conserved. Some core biological processes showed significantly smaller number of conserved TFBSs in human-opossum comparisons, suggesting greater functional divergence. A new measure of efficiency in multi-genome phylogenetic footprinting (BRPR) shows that including human-opossum conservation increases the specificity in finding human TFBSs."

The first marsupial genome sequence [Nature Rev Gen]

"One surprising finding from comparing the opossum and human genomes is that most sequence innovation in the human genome following the eutherian split from the metatherian lineage has occurred in non-coding sequences (20% being lineage-specific in eutherians), rather than in coding sequences (only 1% are absent in metatherians). Many of these non-coding sequences are in regions surrounding important developmental genes, indicating that they are functional regulatory elements. The authors found a high degree of overlap between eutherian-specific sequences and transposable elements (16%), which might have served as a driving force in the evolution of the eutherian genome." The first marsupial genome sequence : Article : Nature Reviews Genetics

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