306 research outputs found
Epigenetic regulation of genes mediated by satellite DNA
No full textEpigenetic regulation of genes mediated by satellite DNA
Isidoro Feliciello, Ivana Akrap, Đurđica Ugarković
Satellite DNA is a highly repetitive DNA, organized in long tandem arrays, located in the heterochromatic regions of chromosomes. Due to intrastrand homologous recombination, elements of satellite DNAs can be excised from their heterochromatin loci and integrate into euchromatin. This scenario was proposed to describe euchromatic dispersion of TCAST, the species-specific major satellite DNA of beetle Tribolium castaneum, which is found associated with numerous protein-coding genes. Dispersed repeats of TCAST (dTcast) were present as monomeric or multimeric repeat units in intragenic (introns), as well as, intergenic regions. Our assumption was that dTcast can influence the expression of associated genes.
Our results show that dTcast does not significantly affect the level of gene expression under physiological condition but induces a transient downregulation of gene transcription after heat stress. Interestingly, also the level of TCAST satellite transcripts in the form of siRNAs and TCAST satellite DNA methylation as well as H3K9 met2/3 in heterochromatin are temperature modulated. We showed a temporary formation of heterochromatic state characterized by increased level of H3K9met2/3 at dTcast insertion sites and their spreading to the proximal regions. Such “heterochromatinization” occurs after heat stress and correlates with transcriptional downregulation of nearby genes. In conclusion, dTcast satellite elements influence the level of expression of their associated genes through RNA interference-based “heterochromatinization” which occurs transiently after heat stress. What is the physiological consequence of this satellite DNA-mediated modulation of gene expression remains to be elucidated
UPAYA KOMUNITAS TALI AKRAP DALAM MENINGKATKAN TOLERANSI ANTAR UMAT BERAGAMA DI KUDUS
No full textKomunitas Lintas Agama dan Kepercayaan Pantura (Tali Akrap) merupakan komunitas yang beranggotakan dari berbagai agama yang ada di Kudus. Adanya Komunitas Tali Akrap karena kurangnya sikap toleransi antar umat beragama. Adanya Komunitas Tali Akrap ini untuk memberikan kesadaran betapa pentingnya kehidupan bertoleransi yang nyata di antara umat beragama yang berbeda-beda. Tujuan penelitian: (1) Mengetahui pandangan Komunitas Tali Akrap terhadap toleransi antar umat beragama, (2) Mengetahui upaya komunitas Tali Akrap dalam meningkatkan toleransi antar umat beragama, (3) Mengetahui faktor pendukung dan faktor penghambat Komunitas Tali Akrap dalam meningkatkan toleransi antar umat beragama di Kudus.
Metode Penelitian yang digunakan adalah Metode Penelitian Kualitatif. Lokasi penelitian di Kantor Seketariat Komunitas Tali Akrap. Subjek dalam penelitian ini adalah Komunitas Tali Akrap. Informan dalam penelitian ini adalah anggota komunitas Tali Akrap, masyarakat dan perwakilan pemerintah Kabupaten Kudus. Teknik pengumpulan data penelitian dengan menggunakan observasi, wawancara dan dokumentasi. Validitas data yang digunakan adalah Teknik Triangulasi Data. Teknik Analisis Data dalam penelitian ini meliputi: pengumpulan data, reduksi data, penyajian data dan pengambilan keputusan atau verifikasi. Penelitian ini menggunakan konsep dialog umat beragama dari Hendropuspito dan multikulturalisme dari Ainul Yaqin.
Hasil penelitian ini menunjukkan bahwa: (1) toleransi adalah saling menyadari perbedaan agama yang ada dengan cara berkumpul bersama menjadi satu keluarga, (2) Upaya komunitas Tali Akrap dalam meningkatkan toleransi antar umat beragama dengan cara melakukan kegiatan rutin, seperti forum diskusi, kemah lintas agama serta peringatan hari keagamaan dan melalui kegiatan insidental dengan melakukan kegiatan pirukun. (3) Faktor pendukung dalam meningkatkan toleransi antar umat beragama yaitu, partisipasi tokoh agama, partisipasi anggota komunitas Tali Akrap, dukungan dari donatur dan dukungan dari pemerintah, sedangkan faktor penghambat dalam meningkatkan toleransi antar umat beragama yaitu kesibukan anggota komunitas Tali Akrap, kecurigaan terhadap agama lain, dan minimnya keterlibatan tokoh agama lain dalam kegiatan komunitas Tali Akrap.
Saran dalam penelitain ini adalah: (1) Bagi Pengurus Komunitas Tali Akrap mensosialisasikan setiap kegiatan yang dilakukan melalui media masa maupun media lainnya serta menambah kegiatan-kegiatan yang lebih menyatu dengan masyarakat, seperti bakti sosial dan kesehatan bagi masyarakat. (2) Bagi Tokoh Agama, turut serta dalam menjaga dan meningkatkan toleransi antar umat beragama, sehingga dapat mengurangi konflik agama. (3) Bagi Masyarakat Kabupaten Kudus, membuka diri dan berinteraksi dengan umat beragama lain, sehingga tidak ada kecurigaan dan toleransi dapat selalu terwujud di masyarakat.
Tali Akrap community is a community has members that consist of various religions. Tali Akrap community located in Kudus. The existance history of Tali Akrap community caused the lack of tolerence among religious people, so the goal of Tali Akrap community that to provides awareness of the important real life tolerance among religious people. This research purposes to know (1) the tolerance of Tali Akrap community that mutual realize about religions difference by assemle each other of members then be a family and mutual respect about others religious rights then help each other as part of loving God. (2) the efforts of Tali Akrap community increasing tolerance among religious people by doing habitual activity, such as discussion forum, cross religious camping, religiuos day celebration, and pirukun as incidental activity. (3) supporting factors to increasing the tolerance are religious leaders participation, member of Tali Akrap community participation, endorsement of donor and goverment. Whereas restricting factors are activity members of Tali Akrap community, mistrust of other religions, and a minimum of other religious leaders inlvolvement for Tali Akrap community activities. Most of the Tali Akrap community activities based on human social that purposed to establish the members to be capable of implementing shared values as religious members, be respect and be sensitive to the other religious rights
FERTILITY AND EMPLOYMENT OF WOMEN IN CROATIA
No full textNegativni učinci niskih stopa fertiliteta izazvale su zabrinutost EU-a, koji u posljednje vrijeme stavlja sve veći naglasak na mjere koje će omogućiti ženama usklađivanje poslovnoga i obiteljskog života, stoga je u kreiranju socijalne politike EU-a velik naglasak stavljen upravo na usklađivanje profesionalnoga i obiteljskog života. Problematika usklađivanja posla i obitelji s demografskog je gledišta važna zbog utjecaja na fertilitet i fertilitetne intencije (Akrap, Čipin, 2010 prema Palomba, 2003).
Prema kulturološkom objašnjenju niskoga fertiliteta, samoispunjenje je glavni cilj u životu, a imanje djece postaje biti sve manje važno u životima pojedinaca i parova. Kao rezultat toga, ulazak u brak i imanje djece odgađaju se za kasnije godine života sve dok se ostali ciljevi u životu, poput stjecanja željene razine obrazovanja i stjecanja zadovoljavajuće pozicije na tržištu rada, ne ostvare (Čipin i Strmota, 2012). Činjenica je da imanje djece u razvijenim zemljama, osobito u uvjetima visoke zaposlenosti žena i njihova visokog stupnja školovanja, povlači za sobom određeni oportunitetni trošak vezan uz odgoj i brigu o djetetu, o njegovu zdravlju, školovanju itd. Stoga životni „partneri“, otac i majka, u takvim životnim i radnim uvjetima često smatraju da imanje djece smanjuje ukupni iznos dohotka koji zarađuju, da im ograničava slobodu trošenja dohotka i slobodu u korištenju slobodnog vremena, da im stvara zapreke u napredovanje na poslu i da smanjuje mogućnosti u postizanju karijere
Correction: Satellite DNA Modulates Gene Expression in the Beetle Tribolium castaneum after Heat Stress.
No full textNon-coding repetitive DNAs have been proposed to perform a gene regulatory role, however for tandemly repeated satellite DNA no such role was defined until now. Here we provide the first evidence for a role of satellite DNA in the modulation of gene expression under specific environmental conditions. The major satellite DNA TCAST1 in the beetle Tribolium castaneum is preferentially located within pericentromeric heterochromatin but is also dispersed as single repeats or short arrays in the vicinity of protein-coding genes within euchromatin. Our results show enhanced suppression of activity of TCAST1-associated genes and slower recovery of their activity after long-term heat stress relative to the same genes without associated TCAST1 satellite DNA elements. The level of gene suppression is not influenced by the distance of TCAST1 elements from the associated genes up to 40 kb from the genes’ transcription start sites, but it does depend on the copy number of TCAST1 repeats within an element, being stronger for the higher number of copies. The enhanced gene suppression correlates with the enrichment of the repressive histone marks H3K9me2/3 at dispersed TCAST1 elements and their flanking regions as well as with increased expression of TCAST1 satellite DNA. The results reveal transient, RNAi based heterochromatin formation at dispersed TCAST1 repeats and their proximal regions as a mechanism responsible for enhanced silencing of TCAST1-associated genes. Differences in the pattern of distribution of TCAST1 elements contribute to gene expression diversity among T. castaneum strains after long-term heat stress and might have an impact on adaptation to different environmental conditions
Epigenetic regulation of genes mediated by satellite DNA
No full textSatellite DNA is a highly repetitive DNA, organized in long tandem arrays, located in the heterochromatic regions of chromosomes. Repeats of satellite DNAs can be excised from their heterochromatin loci and integrate into euchromatin. This scenario was proposed to describe euchromatic dispersion of TCAST1, the species-specific major satellite DNA of beetle Triboliumcastaneum, which is associated with numerous protein-coding genes. Dispersed repeats of TCAST1 (dTcast1) were present as monomeric or multimeric repeat units in intragenic (introns), as well as, intergenic regions. Our assumption was that dTcast1can influence the expression of associated genes.
Our results show that dTcast1 affects the adjacent genes under physiological condition by inducing a slight downregulation of gene expression. The effect is more pronounced after heat stress when transient increase of satellite DNA transcripts processed into TCAST1-siRNAs is induced. We showed that a temporary formation of heterochromatic state characterized by increased level of H3K9met2/3 at dTcast insertion sites and their spreading to the proximal regions is responsible for downregulation of nearby genes. In conclusion, dTcast1 satellite elements influence the level of expression of their associated genes through RNA interference-based „heterochromatinization“and the level of suppression is positively correlated with the amount of transcripts of TCAST1 satellite DNA. Insertion of satellite DNA repeats within euchromatin provides genes with regulatory elements that modulate their activity in particular in response to environmental stress. Variation in satellite repeats insertion among individuals can in some cases provide phenotypic variation that could be acted upon by selection enabling satellite DNA to contribute to the evolution of gene regulatory networks
Satellite DNA as a driver of population divergence in the red flour beetle Tribolium castaneum
No full textTandemly repeated satellite DNAs are among most rapidly evolving sequences in eukaryotic genome, usually differing significantly among closely related species. By inducing changes in heterochromatin and/or centromere, satellite DNAs are expected to drive population and species divergence. However, despite high evolutionary dynamics, divergence of satellite DNA profiles at the level of natural population which precedes and possibly triggers speciation process is not readily detected. Here we characterize minor TCAST2 satellite DNA of the red flour beetle Tribolium castaneum and follow its dynamics among wild-type strains originating from diverse geographic locations. The investigation revealed presence of three distinct subfamilies of TCAST2 satellite DNA which differ in monomer size, genome organization and subfamily-specific mutations. Subfamilies Tcast2a and Tcast2b are tandemly arranged within pericentromeric heterochromatin while Tcast2c is preferentially dispersed within euchromatin of all chromosomes. Among strains, TCAST2 subfamilies are conserved in sequence but exhibit a significant content variability. This results in overrepresentation or almost complete absence of particular subfamily in some strains and enables discrimination between strains. It is proposed that homologous recombination, probably stimulated by environmental stress, is responsible for the emergence of TCAST2 satellite subfamilies, their copy number variation and dispersion within genome. The results represent the first evidence for the existence of population-specific satellite DNA profiles. Partial organization of TCAST2 satellite DNA in the form of single repeats dispersed within euchromatin additionally contributes to the genome divergence at the population level
Delineating cellular heterogeneity and organization of breast cancer stem cells
No full textBreast cancer is characterized by a high degree of heterogeneity in terms of histological, molecular and clinical features, affecting disease progression and treatment response. The cancer stem cell (CSC) model suggests, that cancers are organized in a hierarchical fashion and driven by small subsets of CSCs, endowed with the capacity for self-renewal, differentiation, tumorigenicity, invasiveness and therapeutic resistance. The overall aim of this thesis was to characterize CSC phenotypes and the cellular organization in estrogen receptor α + (ERα+) and ERα- subtypes of breast cancer at the individual cell level. Furthermore, we aimed to identify novel functional CSC markers in a subtype-independent manner, allowing for better identification and targeting of breast-specific CSCs. At present, single-cell quantitative reverse transcription polymerase chain reaction represents the most commonly applied method to study transcript levels in individual cells. Inherent to most single-cell techniques is the difficulty to analyze minute amounts of starting material, which most often requires a preamplification step to multiply transcript copy numbers in a quantitative manner.
In Paper I we have evaluated effects of variations of relevant parameters on targeted cDNA preamplification for single-cell applications, improving reaction sensitivity and specificity, pivotal prerequisites for accurate and reproducible transcript quantification.
In Paper II we have applied single-cell gene expression profiling in combination with three functional strategies for CSC enrichment and identified distinct CSC/progenitor clusters in ERα+ breast cancer. ERα+ tumors display a hierarchical organization as well as different modes of cell transitions. In contrast, ERα- breast cancer show less prominent clustering but share a quiescent CSC pool with ERα+ cancer. This study underlines the importance of taking CSC heterogeneity into account for successful treatment design.
In Paper III we have used a non-biased genome-wide screening approach to identify transcriptional networks specific to CSCs in ERα+ and ERα- subtypes. CSC-enriched models revealed a hyperactivation of the mevalonate metabolic pathway. When detailing the mevalonate pathway, we identified the mevalonate precursor enzyme 3-hydroxy-3-methylglutaryl-CoA synthase 1 (HMGCS1) as a specific marker of CSC-enrichment in ERα+ and ERα- subtypes, highlighting HMGCS1 as a potential gatekeeper for dysregulated mevalonate metabolism important for CSC-features. Pharmacological inhibition of HMGCS1 could therefore be a novel treatment approach for breast cancer patients targeting CSCs
Forster distances for fluorescence resonant energy transfer between mCherry and other visible fluorescent proteins
No full textAkrap N, Seidel T, Barisas BG. Forster distances for fluorescence resonant energy transfer between mCherry and other visible fluorescent proteins. ANALYTICAL BIOCHEMISTRY. 2010;402(1):105-106.We present, for the red fluorescent protein mCherry acting as both fluorescence resonant energy transfer (FRET) donor and acceptor, Forster critical distance (r(0)) values with five important visible fluorescent protein (VFP) variants as well as with itself. The pair EYFP-mCherry exhibits an r(0) of 5.66 nm, equaling or exceeding any combination of VFPs reported previously. Moreover, mCherry should be an excellent chromophore for homo-FRET with an r(0) of 5.10 nm for energy transfer between two mCherry moieties. Finally, mCherry exhibits higher r(0) values than does DsRed. These characteristics, combined with mCherry's rapid folding and excellent spectral properties, suggest that mCherry constitutes a valuable long-wavelength hetero-FRET acceptor and probe for homo-FRET experiments. (C) 2010 Elsevier Inc. All rights reserved
Dispersed satellite DNA elements and their effect on gene expression
No full textDifferent from dispersed transposable elements whose role in evolution of gene regulation was investigated in diverse model organism, influence of satellites DNA on gene regulation was not investigated till now. To perform potential regulatory function, satellite DNA elements are predicted not only to be present within heterochromatin, but to be distributed in euchromatic portion of the genome, in the vicinity of genes. Within insect species Tribolium castaneum satellite DNAs make a substantial portion of the genome and are major constituents of pericentromeric heterochromatin. The expression of a major heterochromatic T. castaneum satellite DNA TCAST1 proceeds in the form of long double-strand transcripts which are rapidly processed into small interfering RNAs (siRNAs). Satellite DNA expression is strongly induced by heat shock, and increased level of satellite-derived siRNAs is accompanied by increase of repressive epigenetic modifications of histones, H3K9me2-3 at satellite DNA regions. Single repeats or short stretches of the same TCAST1 satellite DNA are also dispersed in the close vicinity of protein-coding genes within euchromatin of T. castaneum. To explore the potential gene-regulatory role of TCAST1 satellite elements, we examined variation of TCAST1 elements among 10 T. castaneum wild-type strains originating from diverse geographic locations, and followed expression of genes that either contain or have in the vicinity polymorphic TCAST1 elements. Gene expression was explored at normal as well as under heat stress conditions. Expression analysis of genes that contain polymorphic TCAST1 elements within introns indicates influence of TCAST1 elements on gene expression under heat stress conditions. The gene expression is effected by the presence of TCAST1 element as well as by the number of repeats within dispersed TCAST1 satellite element. In all cases, TCAST1 elements partially repressed activity of genes after heat shock treatment. It is proposed that TCAST1-associated siRNAs, significantly induced after heat stress, affect epigenetic state of euchromatic regions containing dispersed TCAST1 satellite elements by increasing repressive epigenetic modifications of histones. This is the first demonstration of satellite DNA involvement in the modulation of protein-gene expression and indication for the role of satellite DNA in the evolution of gene regulation
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