Találati lista | Tudóstér

001-es BibID:	BIBFORM054433
Első szerző:	Dániel Bence (molekuláris biológus)
Cím:	The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages / Bence Daniel, Gergely Nagy, Nasun Hah, Attila Horvath, Zsolt Czimmerer, Szilard Poliska, Tibor Gyuris, Jiri Keirsse, Conny Gysemans, Jo A. Van Ginderachter, Balint L. Balint, Ronald M. Evans, Endre Barta, Laszlo Nagy
Dátum:	2014
ISSN:	0890-9369
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:	Genes & Development. - 28 : 14 (2014), p. 1562-1577. -
További szerzők:	Nagy Gergely (1986-) (molekuláris biológus) Hah, Nasun Horváth Attila (1988-) (programtervező informatikus) Czimmerer Zsolt (1981-) (molekuláris biológus) Póliska Szilárd (1978-) (biológus) Gyuris Tibor Keirsse, Jiri Gysemans, Conny Van Ginderachter, Jo A. Bálint Bálint László (1971-) (kutató orvos) Evans, Ronald M. Barta Endre (1963-) (molekuláris biológus) Nagy László (1966-) (molekuláris sejtbiológus, biokémikus)
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
Borító:
Saját polcon:

001-es BibID:	BIBFORM065115
Első szerző:	Nagy Gergely (molekuláris biológus)
Cím:	Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA / Gergely Nagy, Erik Czipa, László Steiner, Tibor Nagy, Sándor Pongor, László Nagy, Endre Barta
Dátum:	2016
ISSN:	1471-2164
Megjegyzések:	BACKGROUND:ChIP-seq provides a wealth of information on the approximate location of DNA-binding proteins genome-wide. It is known that the targeted motifs in most cases can be found at the peak centers. A high resolution mapping of ChIP-seq peaks could in principle allow the fine mapping of the protein constituents within protein complexes, but the current ChIP-seq analysis pipelines do not target the basepair resolution strand specific mapping of peak summits.RESULTS:The approach proposed here is based on i) locating regions that are bound by a sufficient number of proteins constituting a complex; ii) determining the position of the underlying motif using either a direct or a de novo motif search approach; and iii) determining the exact location of the peak summits with respect to the binding motif in a strand specific manner. We applied this method for analyzing the CTCF/cohesin complex, which holds together DNA loops. The relative positions of the constituents of the complex were determined with one-basepair estimated accuracy. Mapping the positions on a 3D model of DNA made it possible to deduce the approximate local topology of the complex that allowed us to predict how the CTCF/cohesin complex locks the DNA loops. As the positioning of the proteins was not compatible with previous models of loop closure, we proposed a plausible "double embrace" model in which the DNA loop is held together by two adjacent cohesin rings in such a way that the ring anchored by CTCF to one DNA duplex encircles the other DNA double helix and vice versa.CONCLUSIONS:A motif-centered, strand specific analysis of ChIP-seq data improves the accuracy of determining peak positions. If a genome contains a large number of binding sites for a given protein complex, such as transcription factor heterodimers or transcription factor/cofactor complexes, the relative position of the constituent proteins on the DNA can be established with an accuracy that allow one to deduce the local topology of the protein complex. The proposed high resolution mapping approach of ChIP-seq data is applicable for detecting the contact topology of DNA-binding protein complexes.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban CTCF DNA loop cohesin ChIP-seq
Megjelenés:	BMC Genomics. - 17 : 637 (2016), p. 1-9. -
További szerzők:	Czipa Erik (1990-) (molekuláris biológus, bioinformatikus) Steiner László Nagy Tibor (Gödöllő) Pongor Sándor Nagy László (1966-) (molekuláris sejtbiológus, biokémikus) Barta Endre (1963-) (molekuláris biológus)
Pályázati támogatás:	TÁMOP-4.2.2.C-11/1/KONV-2012-0010 TÁMOP
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
Borító:
Saját polcon:

001-es BibID:	BIBFORM049597
035-os BibID:	PMID:23973299 WOS:000325840200014
Első szerző:	Nagy Gergely (molekuláris biológus)
Cím:	A novel method to predict regulatory regions based on histone mark landscapes in macrophages / Gergely Nagy, Bence Dániel, Dávid Jónás, László Nagy, Endre Barta
Dátum:	2013
ISSN:	0171-2985
Megjegyzések:	Macrophages as phagocytes and professional antigen presenting cells play critical roles in both innate and adaptive immunity. Main transcription factors acting during their differentiation and function are known, but the behavior and co-operation of these factors still remained unexplored. We introduce a new approach to map nucleosome-free regions using exclusively active enhancer and core promoter marking histone modification ChIP-seq data. We could detect approximately 56,000 potential active enhancers/promoters showing different lengths and histone modification shapes. Beside the highly enriched PU.1 and C/EBP sites, we could also detect binding sites for RUNX and AP-1, as well as for the MiT (MITF-TFE) family and MEF2 proteins. The PU.1 and C/EBP transcription factors are known for transforming cells into macrophages. The other transcription factors found in this study can play a role in macrophages as well, since it is known that the MiT family proteins are responsible for phagocytic activity and the MEF2 proteins specify monocytic differentiation over the granulocyte direction. Our results imply that this method can provide novel information about transcription factor organization at enhancers and core promoters as well as about the histone modifications surrounding regulatory regions in any immune or other cell types.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban BWA Burrows-Wheeler Alignment Tool CRE ChIP DMEM Dulbecco's modified Eagle's medium ENCODE Enhancer FAIRE HLH HOMER HTH Histone modification IGV Macrophage NFR NOR Nucleosome-free region PU.1 Promoter SRA TSS bZIP basic leucine zipper cAMP response element chromatin immunoprecipitation encyclopedia of DNA elements formaldehyde-assisted isolation of regulatory elements helix-loop-helix helix-turn-helix hypergeometric optimization of motif EnRichment integrative genomics viewer nucleosome occupied region nucleosome-free region sequence read archive transcription start site
Megjelenés:	Immunobiology. - 218 : 11 (2013), p. 1416-1427. -
További szerzők:	Dániel Bence (1987-) (molekuláris biológus) Jonás Dávid Nagy László (1966-) (molekuláris sejtbiológus, biokémikus) Barta Endre (1963-) (molekuláris biológus)
Pályázati támogatás:	K100196 OTKA TÁMOP422_2012_002 TÁMOP
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
Borító:
Saját polcon: