Identificação e caracterização de regiôes de eucromatina associadas à regulação da expressão gênica e à gordura intramuscular em bovinos da raça Nelore

Em eucariotos, o DNA é organizado juntamente com histonas em um complexo nucleoproteico conhecido como cromatina, cuja unidade fundamental corresponde aos nucleossomos. A cromatina apresenta-se de duas maneiras: eucromatina, região estruturalmente menos condensada e, portanto, mais facilmente transcrita, e heterocromatina, região muito condensada e transcricionalmente silenciosa. Na forma de eucromatina, o acesso dos fatores de transcrição a regiões de DNA livres de nucleossomos é facilitado, enquanto que na forma de heterocromatina os fatores de transcrição não conseguem acessar o DNA para ativar ou reprimir a expressão gênica inferindo, assim, que o grau de compactação da cromatina interfere na regulação da expressão gênica e que o nucleossomo atua como silenciador gênico. Neste contexto, os objetivos foram identificar, mapear e caracterizar regiões em eucromatina na musculatura esquelética de bovinos da raça Nelore. As análises foram realizadas em relação ao músculo Longissimus dorsi pela técnica Assay for Transposase-Accessible Chromatin (ATAC-Seq), capaz de isolar regiões livres de nucleossomos a partir do mecanismo enzimático de transposição. A fim de otimizar o protocolo dessa metodologia para tecido muscular, foram testadas concentrações de 50 mil, 75 mil e 100 mil núcleos tratados com transposase. Destes, foram encontrados 6.811, 11.121 e 11.473 picos de eucromatina, respectivamente, e 6.212 regiões de cromatina aberta foram coincidentes nas três amostras. A associação entre regiões eucromáticas, expressão gênica e gordura intrasmuscular foi confirmada a partir da análise de sobreposição com transcriptional start sites (TSS), genes expressos em músculo esquelético, genes diferencialmente expressos (GDE) para gordura intramuscular e regiões de expression quantitative trait loci (eQTL) de tecido muscular reforçando, assim, o potencial regulatório das regiões de eucromatina.

In eukaryotes, DNA is organized along with histones in nucleoproteins complexes known as chromatin, which has nucleosomes as their fundamental unit. Chromatin exists in two forms: euchromatin, corresponding to a lightly condensed structure and an easily transcribed region, and heterochromatin, a highly condensed and transcriptionally silent region. In euchromatin form, transcription factors have free access to nucleosome-depleted DNA regions, while in heterochromatin the transcription factors can not access the DNA for activate or repress genic expression, which suggests that the chromatin compaction degree interferes with regulation of gene expression and that nucleosomes act as gene silencer. In this context, the aims of the present project were to identify, map and characterize euchromatin regions in the skeletal musculature of Nellore cattle. Analyzes were performed considering the muscle Longissimus dorsi using Assay for Transposase-Accessible Chromatin technique (ATAC-Seq), which isolates nucleosome-depleted regions throught transposition enzymatic mechanism. Differente transposase-treated nuclei concentrations were tested: 50 thousand, 75 thousand and 100 thousand. From these, 6.811, 11.121, and 11.473 euchromatin peaks were found, respectively, and 6.212 open chromatin regions were coincident among them. The association between euchromatic regions, gene expression and intrasmuscular fat was confirmed from the overlap analysis with transcriptional start sites (TSS), genes expressed in skeletal muscle, differentially expressed genes (GDE) for intramuscular fat and regions of expression quantitative trait loci (eQTL) of muscle tissue, reinforcing the regulatory potential of the euchromatin regions.

Cromatina espermática: quebrando paradigmas / Sperm chromatin: breaking paradigms

Há algumas décadas, pensava-se que espermatozoides maduros possuíssem uma cromatina não funcional, inerte, sem a capacidade de transcrição. Acreditava-se que a matriz nuclear não existisse e que a presença de histonas no núcleo seria um erro no processo de compactação cromatínica, o que poderia interferir na fertilidade do macho. Hoje se sabe que, entre as estruturas toroidais, unidades básicas da cromatina espermática altamente compactada, há algumas poucas regiões que contêm sequências de nucleossomos, e estas geralmente estão anexadas a uma matriz nuclear proteica. Os espermatozoides possuem cromatina altamente organizada e são condutores metabolicamente funcionais do genoma masculino, carreando RNAs de diferentes tipos, os quais, tanto quanto os nucleossomos, são importantes sinalizadores epigenéticos paternos e, logo,influenciam o desenvolvimento embrionário inicial. Portanto, alterações cromatínicas podem não somente interferir no processo de fecundação, como principalmente no desenvolvimento embrionário, o que reforça a necessidade da análise da cromatina na avaliação de reprodutores machos.(AU)

Decades ago, it was thought thatspermatozoa had a chromatin nonfunctional, inert, without the abilityto transcription. It was believed in the absence of nuclear matrix and the presence of the core histones would be an error in the chromatin packaging, which could interfere with male fertility. Today we know that between thetoroidal structures, basic units of highly compacted sperm chromatin, there are a few regions containing nucleosome sequences, these usually being attached to a nuclear protein matrix. The sperm chromatin is highly organized and is metabolically functional carrier of male genome, carrying different RNA types, which, along with the nucleosomes are important paternal epigenetic signaling, and influencing early embryonic development. Therefore, chromatin alterations not only interfere with the fertilization process, but also influencethe embryonic development, which reinforces the need for chromatin analysis in the evaluation of breeding males.(AU)

Cromatina espermática: quebrando paradigmas / Sperm chromatin: breaking paradigms

Há algumas décadas, pensava-se que espermatozoides maduros possuíssem uma cromatina não funcional, inerte, sem a capacidade de transcrição. Acreditava-se que a matriz nuclear não existisse e que a presença de histonas no núcleo seria um erro no processo de compactação cromatínica, o que poderia interferir na fertilidade do macho. Hoje se sabe que, entre as estruturas toroidais, unidades básicas da cromatina espermática altamente compactada, há algumas poucas regiões que contêm sequências de nucleossomos, e estas geralmente estão anexadas a uma matriz nuclear proteica. Os espermatozoides possuem cromatina altamente organizada e são condutores metabolicamente funcionais do genoma masculino, carreando RNAs de diferentes tipos, os quais, tanto quanto os nucleossomos, são importantes sinalizadores epigenéticos paternos e, logo,influenciam o desenvolvimento embrionário inicial. Portanto, alterações cromatínicas podem não somente interferir no processo de fecundação, como principalmente no desenvolvimento embrionário, o que reforça a necessidade da análise da cromatina na avaliação de reprodutores machos.

Decades ago, it was thought thatspermatozoa had a chromatin nonfunctional, inert, without the abilityto transcription. It was believed in the absence of nuclear matrix and the presence of the core histones would be an error in the chromatin packaging, which could interfere with male fertility. Today we know that between thetoroidal structures, basic units of highly compacted sperm chromatin, there are a few regions containing nucleosome sequences, these usually being attached to a nuclear protein matrix. The sperm chromatin is highly organized and is metabolically functional carrier of male genome, carrying different RNA types, which, along with the nucleosomes are important paternal epigenetic signaling, and influencing early embryonic development. Therefore, chromatin alterations not only interfere with the fertilization process, but also influencethe embryonic development, which reinforces the need for chromatin analysis in the evaluation of breeding males.

Fine Structure Analysis of White Spot Syndrome Virus of Shrimp

White Spot Syndrome Virus (WSSV) was isolated from diseased shrimps presenting with clinical signs of WSSV infection. The seed virus was identified as WSSV by PCR, and used to inoculate to specific pathogen free (SPF) P. vannamei bloodstocks. WSSV was purified as described by Huang from infected gills from inoculated animals that were homogenized in a blender and partially purified by differential centrifugation. The final purification was carried out using density gradient in 10-40% NaBr and purified virus used for morphological analysis using transmission electron microscopy. A negative staining method using 2% PTA was used for purified virus, and electron staining with lead citrate and uranylacetate was used for ultra thin sections of infected tissues. This analysis determined that i) the spikes of intact virions could be clearly identified on the virion surface and on a partially broken envelopes, ii) the nucleocapsid structures were similar to those previously reported, even though the so called "ring" structure described previously was different and, iii) negative staining of purified WSSV fractions identified nucleosome like structures.(AU)

Fine structure analysis of White Spot Syndrome Virus of shrimp

White Spot Syndrome Virus (WSSV) was isolated from diseased shrimps presenting with clinical signs of WSSV infection. The seed virus was identified as WSSV by PCR, and used to inoculate to specific pathogen free (SPF) P. vannamei bloodstocks. WSSV was purified as described by Huang from infected gills from inoculated animals that were homogenized in a blender and partially purified by differential centrifugation. The final purification was carried out using density gradient in 10-40% NaBr and purified virus used for morphological analysis using transmission electron microscopy. A negative staining method using 2% PTA was used for purified virus, and electron staining with lead citrate and uranylacetate was used for ultra thin sections of infected tissues. This analysis determined that i) the spikes of intact virions could be clearly identified on the virion surface and on a partially broken envelopes, ii) the nucleocapsid structures were similar to those previously reported, even though the so called "ring" structure described previously was different and, iii) negative staining of purified WSSV fractions identified nucleosome like structures.