Hsu SK, Lai WY, Novak J, Lehner F, Jakšić AM, Versace E, Schlötterer C.

Genome Biol. 2024 May 28;25(1):141. doi:10.1186/s13059-024-03285-9

Reproductive isolation arises during laboratory adaptation to a novel hot environment.

“After more than 100 generations of adaptation to a novel high temperature regime, we [...] observed significant mate discrimination between ancestral and hot-evolved populations but not for replicate populations evolved independently to the same selection regime.” “We detected 18 major CHC [(cuticular hydrocarbons)] compounds across both sexes, which differ in length of carbon chain or numbers of double bonds” “similar modifications in CHC compositions have been documented for multiple Drosophila species in latitudinal clines, implying that the same causal link with temperature adaptation is also present in natural populations.” “Crosses between replicates of the evolved populations produced on average 8.3% fewer viable offspring than crosses within the same replicates of the evolved populations”

Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM.

PLoS Biol. 2007 Jun;5(6):e152. doi:10.1371/journal.pbio.0050152

Principles of genome evolution in the Drosophila melanogaster species group.

“the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences” “We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group” “The overall rate of breakage in the D. melanogaster / D. yakuba lineage is 0.0183/Mb/Myr.”

Suvorov A, Kim BY, Wang J, Armstrong EE, Peede D, D'Agostino ERR, Price DK, Waddell P, Lang M, Courtier-Orgogozo V, David JR, Petrov D, Matute DR, Schrider DR, Comeault AA.

Curr Biol. 2022 Jan 10;32(1):111-123.e5. doi:10.1016/j.cub.2021.10.052

Widespread introgression across a phylogeny of 155 Drosophila genomes.

2,791 BUSCOs extracted from 155 genomes (149 species) to compute a phylogenetic tree. Introgressions were studied in 9 clades.

Ranz JM, González PM, Su RN, Bedford SJ, Abreu-Goodger C, Markow T.

Proc Biol Sci. 2022 Jan 26;289(1967):20212183. doi:10.1098/rspb.2021.2183

Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera.

Uses 5 to 7000 1-to-1 orthologues to study synteny in insects that speciated ~100 My ago. Uses a definition of microsynteny with no constrains on orientation, where transposition does not interrupt synteny, and where triplets of orthologues do not need to be in the same order. A repurposed tissue-specificity index identifies ancestral relationships between chromosomes. Searched for conserved clusters (Hox etc.) by allowing a distance of 250 kbp between genes, regardless the number of interveining genes. Found that most clusters still exist, but rearranged.

Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM.

Genetics. 2008 Jul;179(3):1657-80. doi:10.1534/genetics.107.086108

Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes.

“This analysis reveals between 42 (D. sechellia) and 1430 (D. willistoni) syntenic blocks across various species on the basis of the D. melanogaster gene order.” “Comparison of syntenic blocks across this large genomic data set confirms that genetic elements are largely (95%) localized to the same Muller element across genus Drosophila species and paracentric inversions serve as the dominant mechanism for shuffling the order of genes along a chromosome.” “When we infer that a breakpoint is reused we mean that two or more breakage events occurred within the nucleotide interval between blocks, but the events are not necessarily coincident within the breakpoint”

Mathog D, Hochstrasser M, Gruenbaum Y, Saumweber H, Sedat J.

Nature. 1984 Mar 29-Apr 4;308(5958):414-21. doi:10.1038/308414a0

Characteristic folding pattern of polytene chromosomes in Drosophila salivary gland nuclei.

Drosophila polytene chromosome arms form isolated topoplogical domains in interphase. Centromeres are clustered near the nuclear enveloppe and telomeres tend to be on the opposite side (the Rabl conformation).

Delprat A, Negre B, Puig M, Ruiz A.

PLoS One. 2009 Nov 18;4(11):e7883. doi:10.1371/journal.pone.0007883

The transposon Galileo generates natural chromosomal inversions in Drosophila by ectopic recombination.

In D. buzzatii, the 2z(3) inversion is flanked by several transposable elements, among which two Galileo repeats (cut-and-paste mechanism, members of the P element family), that “(i) are inserted in opposite orientation; (ii) present exchanged target site duplications; and (iii) are both chimeric”, suggesting ectopic recombination.

Theodosius Dobzhansky and Carl Epling

Carnegie Institution of Washington publicatino 554, Washington, D. C., March 31st, 1944

Contributions to the Genetics, Taxonomy, and Ecology of Drosophila pseudoobscura and its relatives.

“It is certain that if any kind of structural difference had been known between D. pseudoobscura and D. persimilis, they would have been classed as species from the start. Calling them races, and designating them by the letters A and B instead of by Latin names, was an attempt to appease conservative taxonomists who continue to adhere to the purely morphological concepts of species and race. Such a course is neither scientifically consistent nor practically sound. The species is the stage in the process of evolutionary divergence at which an array of populations once actually interbreeding or capable of interbreeding has become split into two or more reproductively isolated arrays. Species exist in nature regardless of whether we can or cannot distinguish them by their structural characters. There is no doubt that the great majority of animal and plant species differ structurally, and that they can be conveniently, and in most cases readily, recognized and delimited by their morphology alone. But it does not follow that any and all species are recognizable by their externally visible structures.”

https://books.google.com/books?id=J1A1AAAAMAAJ

Machado CA, Haselkorn TS, Noor MA.

Genetics. 2007 Mar;175(3):1289-306. doi:10.1534/genetics.106.064758

Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in Drosophila pseudoobscura and D. persimilis.

“suppression of crossovers in inversion heterozygotes also extends to loci located outside the inversion but close to it (within 1–2 Mb)”

Rizki MT

Proc Natl Acad Sci U S A. 1951 Mar;37(3):156-9. doi:10.1073/pnas.37.3.156

Morphological differences between two sibling species; Drosophila pseudoobscura and Drosophila persimilis.

The first morphological difference that distinguishes D. persimilis from D. pseudoobscura: penis size.

Dobzhansky T, Sturtevant AH

Genetics. 1938 Jan;23(1):28-64. doi:10.1093/genetics/23.1.28

Inversions in the Chromosomes of Drosophila Pseudoobscura.

Observation of polytene chromosomes in salivary glands of hybrid D. pseudoobscura crossed form different populations showed lage-scale inversions in the 3rd chromosome. The collection of haplotypes can be represented as a graph linking single inversion events. Multiple haplotypes may coexist in the same geographical region.

Crapse J, Pappireddi N, Gupta M, Shvartsman SY, Wieschaus E, Wühr M.

Mol Syst Biol. 2021 Aug;17(8):e9895. doi: 10.15252/msb.20209895

Arrhenius equation for developmental processes.

Fitting development time courses at different temperatures to the Arrhenius law shows that different steps have different activation energies. The fit is not linear, and the fact that each step is a combination of many reactions is not enough to explain the extent of the deviation. In addition, the fit of simple reactions catalysed by GAPDH or LacZ is also non-linear. The authors postulate that “Either all rate-limiting steps occurring in parallel at a given embryonic stage have evolved similar activation energies, or the embryos have developed checkpoints that assure a resynchronization of converging developmental processes over wide temperature ranges.”

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18. doi:10.1038/nature06341

Evolution of genes and genomes on the Drosophila phylogeny.

The result of pairwise comparisons between the species ranges between a few tens or hundreds of synteny blocks of up to ~1000 genes, to ~1000 synteny blocks with a few (tens of) genes.

Schlötterer C, Hauser MT, von Haeseler A, Tautz D.

Mol Biol Evol. 1994 May;11(3):513-22. doi:10.1093/oxfordjournals.molbev.a040131

Comparative evolutionary analysis of rDNA ITS regions in Drosophila.

Average substitution rate of 1.2% per million year.

Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ.

Genome Res. 2021 Feb 9. doi:10.1101/gr.263442.120

Evolution of genome structure in the Drosophila simulans species complex.

“de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago.” “Genome-wide, ∼15% of sim-complex genome content fails to align uniquely to D. melanogaster.” “Within aligned sequence blocks, the sim-complex species show ∼7% divergence from D. melanogaster” “535–542 rearrangements between D. melanogaster and the sim-complex (approximately 90 mutations per million years), and 113–177 rearrangements within the sim-complex (226–354 mutations per million years)”

Fuqua T, Jordan J, van Breugel ME, Halavatyi A, Tischer C, Polidoro P, Abe N, Tsai A, Mann RS, Stern DL, Crocker J.

Nature. 2020 Nov;587(7833):235-239. doi:10.1038/s41586-020-2816-5

Dense and pleiotropic regulatory information in a developmental enhancer

Study of the E3N enhancer of the shavenbaby (svb) gene. Immunohistochemistry automated with liquid handling robots. “sequence conservation is not an accurate predictor of the quantitative roles of individual sites in the E3N enhancer” “most mutations in E3N led to changes in transcriptional outputs, suggesting that regulatory information is distributed densely within this enhancer”

Ranz JM, Casals F, Ruiz A.

Genome Res. 2001 Feb;11(2):230-9. doi:10.1101/gr.162901

How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila.

186 DNA probes on Muller element E (density: 1 / 175 kbp in D. mel and 1 / 219 in D. rep) for comparing gene order in D. repleta and D. melanogaster. Random distribution of breakpoints. “177.07 (±28.88) breakpoints or 89 (±14) paracentric inversions fixed in this chromosomal element between D. melanogaster and D. repleta.” “Application of [a] ML method [...] yielded an estimate of 228 (±28) fixed breakpoints, that is, 114 ± 14 fixed inversions.” “We estimate an evolution rate of 0.9–1.4 chromosomal inversions fixed per million years.” “A significant correlation of gene order was found.” “If large inversions have a low probability of fixation because of their fertility effects (Navarro et al. 1997), which seems to be the case (Cáceres et al. 1997), then the randomization of gene order would proceed at a slower rate than is implied in Figure 2.”

Bracewell R, Tran A, Chatla K, Bachtrog D.

G3 (Bethesda). 2020 Mar 5;10(3):891-897. doi:10.1534/g3.119.400922

Chromosome-Level Assembly of Drosophila bifasciata Reveals Important Karyotypic Transition of the X Chromosome.

Chromosome arms do not interact much with each other. Large and highly repetitive pericentric regions in which it is hard to map the Hi-C reads.

Schneider I.

J Embryol Exp Morphol. 1972 Apr;27(2):353-65.

Cell lines derived from late embryonic stages of Drosophila melanogaster.

“At least one line is derived from imaginal disc cells.” As reported for other insects, cell spheres appeared in the cultures after 2–3 weeks. At each passage, spheres are trypsinised or simple teased apart.

Echalier G, Ohanessian A.

C R Acad Hebd Seances Acad Sci D. 1969 Mar 31;268(13):1771-3.

https://gallica.bnf.fr/ark:/12148/bpt6k62969219/f623.image

Spontaneous transformation after multiple months of culture.

Schaeffer SW

Genetics. 2018 Sep;210(1):3-13. doi:10.1534/genetics.118.301084

Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics.

Review

Proc Natl Acad Sci U S A. 1917 Sep;3(9):555-8 doi:10.1073/pnas.3.9.555

Sturtevant AH

Genetic Factors Affecting the Strength of Linkage in Drosophila.

Chromosomal inversions (not recognised as such at the time) strongly reduce crossing overs in their vicinity.

Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G.

Cell. 2012 Feb 3;148(3):458-72. doi:10.1016/j.cell.2012.01.010

Three-dimensional folding and functional organization principles of the Drosophila genome.

Co-clustering of the centromeres.

Stadler MR, Haines JE, Eisen MB.

Elife. 2017 Nov 17;6. pii: e29550. doi:10.7554/eLife.29550

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo.

High-resolution Hi-C analysis of Drosophila chromosomes in Rabl conformation during embryogenesis. “We propose a model in which insulators achieve domain separation by lowering the compaction ratio of bound chromatin, thereby converting the short lengths of insulator DNA (measured in base pairs) into large relative physical distances.”

Russo CA, Takezaki N, Nei M.

Mol Biol Evol. 1995 May;12(3):391-404 doi:10.1093/oxfordjournals.molbev.a040214

Molecular phylogeny and divergence times of drosophilid species.

Study of Adh genes, nuclear 18S rRNA and mitochondrial DNA suggests that D. mel and D. pseudoobscura diverged 24.9 +/- 2.88 My ago, based on the assumption that D. picticornis and D. silvestris diverged 5.1 My ago.

Beckenbach AT, Wei YW, Liu H.

Mol Biol Evol. 1993 May;10(3):619-34 doi:10.1093/oxfordjournals.molbev.a040034

Relationships in the Drosophila obscura species group, inferred from mitochondrial cytochrome oxidase II sequences.

Analysis of Cox2 sequences of Drosophila species is most compatible with a speciation of D. melanogaster and D. pseudoobscura ~35 My ago. Sequence divergence between D. mel. and members of the D. obscura species group is in average of 11.4 %.

Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM.

Nat Genet. 2019 Aug;51(8):1272-1282. doi:10.1038/s41588-019-0462-3

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.

Sequencing of balancer chromosomes. Allele-specific RNA-seq, Hi-C and Capture-C. “Genes with changes in their expression have a small but significant enrichment for differential promoter contacts”, but the converse is not true. “Loss of long-range chromatin loops has little impact on gene expression.”

Long E, Evans C, Chaston J, Udall JA.

G3 (Bethesda). 2018 Oct 3;8(10):3247-3253. doi:10.1534/g3.118.200631

Genomic Structural Variations Within Five Continental Populations of Drosophila melanogaster.

Compares breakpoint position with a +-3 bp tolerance. Uses Assemblytics.

Frith MC, Kawaguchi R.

Genome Biol. 2015 May 21;16:106. doi:10.1186/s13059-015-0670-9

Split-alignment of genomes finds orthologies more accurately.

Optimal set of local alignments. Striking example of intra-chromosomal loss of synteny between D. melanogaster and D. pseudoobscura. Heuristic approach inspired by the “repeated matches algorithm” of Durbin and coll., 1998.

Genes Dev. 1988 Jun;2(6):754-65.

Beyer AL, Osheim YN.

Splice site selection, rate of splicing, and alternative splicing on nascent transcripts.

Chromatin spread illustrating alternative splicing.

G3 (Bethesda). 2018 Aug 7. pii: g3.200160.2018. doi:10.1534/g3.118.200160

Miller DE, Staber C, Zeitlinger J, Hawley RS.

Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing.

29× coverage and N50 of 4.4. Mb in average. A multiplexed NextSeq 500 run was used for polishing. Optimisation of Nanopore throughput by reorganising pore groups periodically, extracting high molecular weight DNA with phenol/chloroform extration, and using more DNA in the library preparation. Benchmark of various tools including minimap/miniasm and canu.

Sci Rep. 2018 Jun 22;8(1):9500. doi:10.1038/s41598-018-27805-3

Lajbner Z, Pnini R, Camus MF, Miller J, Dowling DK.

Experimental evidence that thermal selection shapes mitochondrial genome evolution.

Experimental evidence for the “mitochondrial climatic hypothesis”. Haplotypes only differ by non-coding or synonymous changes. Wolbachia infection was a confounding factor and needed to be removed by antibiotic treatment.

G3 (Bethesda). 2018 Jul 17. pii: g3.200162.2018. doi:10.1534/g3.118.200162

Solares EA, Chakraborty M, Miller DE, Kalsow S, Hall K, Perera AG, Emerson JJ, Hawley RS.

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing.

Hybrid de novo assembly (Nanopore / Illumina / Optical) of the Drosophila genome reaches a high (>98%) « BUSCO » score typical of high-quality mainstream reference assemblies. (BUSCO stands for « Benchmarking Universal Single-Copy Orthologs ».)

Kramer MC, Liang D, Tatomer DC, Gold B, March ZM, Cherry S, Wilusz JE

Genes Dev. 2015 Oct 15;29(20):2168-82. doi:10.1101/gad.270421.115

Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins.

Also describes a vector for circularisation of arbitrary exon sequences.

Phadnis N, Baker EP, Cooper JC, Frizzell KA, Hsieh E, de la Cruz AF, Shendure J, Kitzman JO, Malik HS.

Science. 2015 Dec 18;350(6267):1552-5. doi:10.1126/science.aac7504

An essential cell cycle regulation gene causes hybrid inviability in Drosophila.

ENU screen identified 6 rescued males out of > 300,000 offsprings; a single gene was mutated in all 6 mutants.

Xu H, Sepúlveda LA, Figard L, Sokac AM, Golding I.

Nat Methods. 2015 Aug;12(8):739-742. doi:10.1038/nmeth.3446

Combining protein and mRNA quantification to decipher transcriptional regulation.

Analysis of > 21,000 loci from 31 drosophila embryos. Cooperative binding of 6 Bcd molecules to the hb locus. Even at highest Bcd concentration, the gene is inactive roughly half of the time.

Southall TD, Davidson CM, Miller C, Carr A, Brand AH.

Dev Cell. 2014 Mar 31;28(6):685-96. doi:10.1016/j.devcel.2014.01.030

Dedifferentiation of Neurons Precedes Tumor Formation in lola Mutants.

Lola-N isoform prevents neurons from re-entering the cell cycle.

Salzler HR, Tatomer DC, Malek PY, McDaniel SL, Orlando AN, Marzluff WF, Duronio RJ.

Dev Cell. 2013 Mar 25;24(6):623-34. doi: 10.1016/j.devcel.2013.02.014.

A Sequence in the Drosophila H3-H4 Promoter Triggers Histone Locus Body Assembly and Biosynthesis of Replication-Coupled Histone mRNAs.

Transcription is required for assembly of HLB.

Introduces promoter ‘shape index’, finds tags aligning to mitochondrial genome, and suggests that, because they do not overlap with the small RNAs produced by PolII stalling, the 3′ peaks are a processing product.

Hybrid experiment found cases of trans-splicing, but few.

Parry TJ, Theisen JW, Hsu JY, Wang YL, Corcoran DL, Eustice M, Ohler U, Kadonaga JT.

Genes Dev. 2010 Sep 15;24(18):2013-8. doi:10.1101/gad.1951110

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery.

“A specialized TCT-based transcription system that is directed toward the synthesis of ribosomal proteins.”

The atonal sensory organ precursor enhancer (SOPE)