The Epigenome of Evolving Drosophila Neo-Sex Chromosomes: Dosage Compensation and Heterochromatin Formation

Sex chromosomes originated from autosomes but have evolved a highly specialized chromatin structure. Drosophila Y chromosomes are composed entirely of silent heterochromatin, while male X chromosomes have highly accessible chromatin and are hypertranscribed as a result of dosage compensation. Here, we dissect the molecular mechanisms and functional pressures driving heterochromatin formation and dosage compensation of the recently formed neo-sex chromosomes of Drosophila miranda. We show that the onset of heterochromatin formation on the neo-Y is triggered by an accumulation of repetitive DNA. The neo-X has evolved partial dosage compensation and we find that diverse mutational paths have been utilized to establish several dozen novel binding consensus motifs for the dosage compensation complex on the neo-X, including simple point mutations at pre-binding sites, insertion and deletion mutations, microsatellite expansions, or tandem amplification of weak binding sites. Spreading of these silencing or activating chromatin modifications to adjacent regions results in massive mis-expression of neo-sex linked genes, and little correspondence between functionality of genes and their silencing on the neo-Y or dosage compensation on the neo-X. Intriguingly, the genomic regions being targeted by the dosage compensation complex on the neo-X and those becoming heterochromatic on the neo-Y show little overlap, possibly reflecting different propensities along the ancestral chromosome that formed the sex chromosome to adopt active or repressive chromatin configurations. Our findings have broad implications for current models of sex chromosome evolution, and demonstrate how mechanistic constraints can limit evolutionary adaptations. Our study also highlights how evolution can follow predictable genetic trajectories, by repeatedly acquiring the same 21-bp consensus motif for recruitment of the dosage compensation complex, yet utilizing a diverse array of random mutational changes to attain the same phenotypic outcome

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function

An assessment of histone-modification antibody quality

We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/)

Identification of functional elements and regulatory circuits by Drosophila modENCODE

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation

Picosecond Pulsed-Periodic High-Peak Power Nd:YAG Laser Operationally Controlled by KTP-Based Pockels Cell

Electro-optical modulators are effectively used for ultrafast pulse lasers operation control. The scheme of picosecond pulse-periodic high-peak-power Nd:YAG lasers is composed of an active-passive mode-locked and negative feedback-controlled master oscillator and regenerative amplifier based on common end-diode-pumped Nd:YAG crystal. A double-crystal thermally compensated Pockels cell based on KTP crystals of the Y-cut direction is employed as a key control element. The cell was assembled using a pair of equal-length crystals grown according to high-resistivity technology. The scheme provides output pulses with energy up to 1.6 mJ, a duration of 25 ps at repetition rates tunable from 0 to 200 Hz. The laser operation stages are analyzed in detail. The scheme looks attractive and promising for developing advanced ultrafast laser systems with higher repetition rates, peak and, accordingly, average power levels. The Pockels cell based on KTP crystals expands the line of available fast electro-optical control elements, along with the previously used RTP ones. The factors limiting laser pulse energy and repetition rate are discussed. Parasitic nonlinear conversion in the crystals of the Pockels cell along the axis may play an essential role. The results of comparative measurements of the second and third harmonics made with the Pockels cells based on KTP and RTP crystals of both X-cut and Y-cut directions are presented. The minimum second and third harmonics efficiency levels observed in the Y-cut Pockels cells of the KTP crystal seem to be their important advantage

Heterostructure InGaAlAs/InAlAs on the InP substrate for the electro-optical modulator based on the quantum confined Stark effect

The energy structure and the value of the electrooptic effect in heteroepitaxial structures (HES) with multiple InGaAlAs / InAlAs quantum wells have been studied. The interferometric method has been developed to determine small changes in the refractive index under transverse transmission of light through a layered structure. The length of the Mach-Zehnder interferometer for the modulator at HES with multiple InGaAlAs / InAlAs quantum wells has been chosen