Functional characterization of regulatory sequences targeted by the transcription factor SOX2, identified by studies of long-range chromatin interactions in brain-derived neural stem/precursor cells

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العنوان:	Functional characterization of regulatory sequences targeted by the transcription factor SOX2, identified by studies of long-range chromatin interactions in brain-derived neural stem/precursor cells
المؤلفون:	FAVARO, REBECCA, Bertolini, J, NICOLIS, SILVIA KIRSTEN, BERTOLINI, JESSICA ARMIDA
بيانات النشر:	Università degli Studi di Milano-Bicocca country:Italy 2015-06-25
نوع الوثيقة:	Electronic Resource
مستخلص:	Sox2 codifica per un fattore trascrizionale necessario per la pluripotenza delle cellule staminali embrionali. Mutazioni eterozigoti in Sox2 nell’uomo causano difetti nello sviluppo dell’occhio (anoftalmia, microftalmia) e dell’ippocampo, con insorgenza di patologie come epilessia, problemi nel controllo motorio e difetti di apprendimento. Tramite “knock-out” condizionale di Sox2 in topo, abbiamo osservato l’importanza di Sox2 per lo sviluppo del cervello e per il “self-renewal” delle staminali neurali. Di recente è emerso che elementi regolatori possono trovarsi molto lontano dai geni che controllano lungo il cromosoma. Mutazioni in tali elementi talvolta causano patologie dovute a deregolazione del gene associato. In collaborazione con la Dr. C.-L. Wei (California), abbiamo comparato le interazioni “long-range” nella cromatina di cellule di precursori neurali (NPCs) di topi “wild-type” (wt) e Sox2-deleti, usando la tecnica ChIA-PET: su 7000 interazioni mappate in NPCs wt, 2700 erano perse in NPCs Sox2-delete. Tra queste 2700 interazioni, molte coinvolgevano geni legati allo sviluppo neurale e sequenze identificate come enhancer telencefalici per la presenza di siti di legame per p300. Abbiamo poi determinato la mappa genomica dei siti di legame per SOX2 nella cromatina di NPCs wt (in collaborazione con il Dr. F. Guillemot; Londra). Circa metà delle interazioni “long-range” SOX2-dipendenti presentava un picco di ChIP-seq per SOX2, suggerendo un ruolo diretto di SOX2 nel loro mantenimento. Il mio progetto di tesi intende definire se sequenze distali, associate in modo SOX2-dipendente a geni neurali (candidati “target” per SOX2), sono elementi di regolazione trascrizionale attivi durante lo sviluppo embrionale del cervello e se la loro attività è regolata da SOX2. Abbiamo selezionato 13 putativi elementi regolatori distali (DREs), tra le interazioni ChIA-PET perse nelle NPCs Sox2-delete, per caratterizzarli funzionalmente in esperimenti di transgenesi in zebrafis Sox2 encodes a transcription factor required for embryonic stem cell pluripotency. Heterozygous Sox2 mutations in humans cause defects in the development of eyes (anophthalmia, microphthalmia) and hippocampus, with neurological pathology including epilepsy, motor control problems and learning disabilities. Using a Sox2 conditional knock-out in mouse, we discovered that Sox2 is important for brain development and for neural stem cell maintenance. Recently, it was found that transcriptional regulatory elements are not always localized in proximity of the gene they control, but often they lie very far from it on the linear chromosome map. Mutations in these elements can cause pathology, due to the deregulation of the associated gene. In collaboration with Dr. C.-L. Wei’s lab (California), we compared long-range DNA interactions in chromatin of wild-type mouse neural stem/precursor cells (NPCs) and Sox2-deleted cells, using the ChIA-PET technique: out of a total of 7000 long-range interactions mapped in wild-type NPCs, 2700 were lost in Sox2-deleted cells. Many of the lost interactions involved genes important for neural development and sequences already identified as forebrain enhancers by p300 binding in mouse developing telencephalon. In parallel, we determined the genome-wide map of SOX2 binding sites in chromatin of wild-type NPCs, by ChIP-seq (in collaboration with Dr. F. Guillemot; London). At least half of the SOX2-dependent long-range interactions contain a SOX2 ChIP-seq peak, suggesting that SOX2 has a direct role in their maintenance. My project seeks to define if distal sequences, associated in a SOX2-dependent way to neural genes (candidates to be putative SOX2 targets), represent transcriptional regulatory elements active during embryonic brain development and if their activity is regulated by SOX2. We selected 13 putative distal regulatory elements (DREs), among the ChIA-PET interactions lost in Sox2-deleted cells, to functionally characterize them in tra
مصطلحات الفهرس:	Sox2, elementi regolatori distali, zebrafish, distal regulatory element, BIO/18 - GENETICA, info:eu-repo/semantics/doctoralThesis
URL:	http://hdl.handle.net/10281/83922 alleditors:FAVARO, REBECCA
الاتاحة:	Open access content. Open access content info:eu-repo/semantics/openAccess
ملاحظة:	English
Other Numbers:	ITBAO oai:boa.unimib.it:10281/83922 1364258732
المصدر المساهم:	BICOCCA OPEN ARCH From OAIster®, provided by the OCLC Cooperative.
رقم الانضمام:	edsoai.on1364258732
قاعدة البيانات:	OAIster

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