Publications
194 results found
Zuin J, Franke V, van IJcken WFJ, et al., 2014, A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS, PLOS GENETICS, Vol: 10, ISSN: 1553-7404
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- Citations: 93
Plessy C, Pascarella G, Bertin N, et al., 2014, Promoter architecture of mouse olfactory receptor genes, 22nd Congress of the European-Chemoreception-Research-Organization (ECRO), Publisher: OXFORD UNIV PRESS, Pages: 79-79, ISSN: 0379-864X
Mathelier A, Zhao X, Zhang AW, et al., 2014, JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles, NUCLEIC ACIDS RESEARCH, Vol: 42, Pages: D142-D147, ISSN: 0305-1048
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- Citations: 770
Seitan VC, Faure AJ, Zhan Y, et al., 2013, Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments, GENOME RESEARCH, Vol: 23, Pages: 2066-2077, ISSN: 1088-9051
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- Citations: 234
Stadhouders R, Aktuna S, Thongjuea S, et al., 2013, <i>HBS1L</i>-<i>MYB</i> intergenic Variants Modulate Fetal Hemoglobin Via Long-Range <i>MYB</i> Enhancers, 55th Annual Meeting of the American-Society-of-Hematology, Publisher: AMER SOC HEMATOLOGY, ISSN: 0006-4971
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- Citations: 1
Nepal C, Hadzhiev Y, Previti C, et al., 2013, Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis, GENOME RESEARCH, Vol: 23, Pages: 1938-1950, ISSN: 1088-9051
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- Citations: 81
Frangini A, Sjoeberg M, Roman-Trufero M, et al., 2013, The Aurora B Kinase and the Polycomb Protein Ring1B Combine to Regulate Active Promoters in Quiescent Lymphocytes, MOLECULAR CELL, Vol: 51, Pages: 647-661, ISSN: 1097-2765
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- Citations: 84
Armant O, Maerz M, Schmidt R, et al., 2013, Genome-wide, whole mount <i>in situ</i> analysis of transcriptional regulators in zebrafish embryos, DEVELOPMENTAL BIOLOGY, Vol: 380, Pages: 351-362, ISSN: 0012-1606
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- Citations: 43
Harmston N, Lenhard B, 2013, Chromatin and epigenetic features of long-range gene regulation, NUCLEIC ACIDS RESEARCH, Vol: 41, Pages: 7185-7199, ISSN: 0305-1048
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- Citations: 77
Thongjuea S, Stadhouders R, Grosveld FG, et al., 2013, r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data, NUCLEIC ACIDS RESEARCH, Vol: 41, ISSN: 0305-1048
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- Citations: 66
Ghamari A, van de Corput MPC, Thongjuea S, et al., 2013, In vivo live imaging of RNA polymerase II transcription factories in primary cells (vol 27, pg 767, 2013), GENES & DEVELOPMENT, Vol: 27, Pages: 1434-1434, ISSN: 0890-9369
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- Citations: 1
Ghamari A, van de Corput MPC, Thongjuea S, et al., 2013, In vivo live imaging of RNA polymerase II transcription factories in primary cells (vol 27, pg 767, 2013), GENES & DEVELOPMENT, Vol: 27, Pages: 1216-1216, ISSN: 0890-9369
Sheffield NC, Thurman RE, Song L, et al., 2013, Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions, GENOME RESEARCH, Vol: 23, Pages: 777-788, ISSN: 1088-9051
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- Citations: 141
Carvalho RH, Hou J, Haberle V, et al., 2013, Genomewide DNA Methylation Analysis Identifies Novel Methylated Genes in Non-Small-Cell Lung Carcinomas, JOURNAL OF THORACIC ONCOLOGY, Vol: 8, Pages: 562-573, ISSN: 1556-0864
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- Citations: 23
Mylona A, Andrieu-Soler C, Thongjuea S, et al., 2013, Genome-wide analysis shows that <i>Ldb1</i> controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis, BLOOD, Vol: 121, Pages: 2902-2913, ISSN: 0006-4971
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- Citations: 26
Ghamari A, van de Corput MPC, Thongjuea S, et al., 2013, In vivo live imaging of RNA polymerase II transcription factories in primary cells, GENES & DEVELOPMENT, Vol: 27, Pages: 767-777, ISSN: 0890-9369
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- Citations: 102
Danks G, Campsteijn C, Parida M, et al., 2013, OikoBase: a genomics and developmental transcriptomics resource for the urochordate <i>Oikopleura dioica</i>, NUCLEIC ACIDS RESEARCH, Vol: 41, Pages: D845-D853, ISSN: 0305-1048
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- Citations: 44
Harmston N, Barešić A, Lenhard B, 2013, The mystery of extreme non-coding conservation, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 368
Regions of several dozen to several hundred base pairs of extreme conservation have been found in non-coding regions in all metazoan genomes. The distribution of these elements within and across genomes has suggested that many have roles as transcriptional regulatory elements in multi-cellular organization, differentiation and development. Currently, there is no known mechanism or function that would account for this level of conservation at the observed evolutionary distances. Previous studies have found that, while these regions are under strong purifying selection, and not mutational coldspots, deletion of entire regions in mice does not necessarily lead to identifiable changes in phenotype during development. These opposing findings lead to several questions regarding their functional importance and why they are under strong selection in the first place. In this perspective, we discuss the methods and techniques used in identifying and dissecting these regions, their observed patterns of conservation, and review the current hypotheses on their functional significance.
de Santiago I, Brookes E, Morris KJ, et al., 2012, Polycomb complexes co-associate with a specific RNA polymerase II variant inES cells, Collaborative Congress of the European-Society-of-Gene-and-Cell-Therapy/French-Society-of-Cell-and-Gene-Therapy, Publisher: MARY ANN LIEBERT INC, Pages: A20-A20, ISSN: 1043-0342
van Riel B, Pakozdi T, Brouwer R, et al., 2012, A Novel Complex, RUNX1-MYEF2, Represses Hematopoietic Genes in Erythroid Cells, MOLECULAR AND CELLULAR BIOLOGY, Vol: 32, Pages: 3814-3822, ISSN: 0270-7306
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- Citations: 29
Thurman RE, Rynes E, Humbert R, et al., 2012, The accessible chromatin landscape of the human genome, NATURE, Vol: 489, Pages: 75-82, ISSN: 0028-0836
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- Citations: 1806
Carvalho RH, Haberle V, Hou J, et al., 2012, Genome-wide DNA methylation profiling of non-small cell lung carcinomas, EPIGENETICS & CHROMATIN, Vol: 5
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- Citations: 52
Sleutels F, Soochit W, Bartkuhn M, et al., 2012, The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner, EPIGENETICS & CHROMATIN, Vol: 5, ISSN: 1756-8935
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- Citations: 64
Schroder K, Irvine KM, Taylor MS, et al., 2012, Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: E944-E953, ISSN: 0027-8424
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- Citations: 219
Lenhard B, Sandelin A, Carninci P, 2012, REGULATORY ELEMENTS Metazoan promoters: emerging characteristics and insights into transcriptional regulation, NATURE REVIEWS GENETICS, Vol: 13, Pages: 233-245, ISSN: 1471-0056
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- Citations: 335
Plessy C, Pascarella G, Bertin N, et al., 2012, Promoter architecture of mouse olfactory receptor genes, GENOME RESEARCH, Vol: 22, Pages: 486-497, ISSN: 1088-9051
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- Citations: 46
Stadhouders R, Thongjuea S, Andrieu-Soler C, et al., 2012, Dynamic long-range chromatin interactions control <i>Myb</i> proto-oncogene transcription during erythroid development, EMBO JOURNAL, Vol: 31, Pages: 986-999, ISSN: 0261-4189
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- Citations: 106
Taniya T, Tanaka S, Yamaguchi-Kabata Y, et al., 2012, A prioritization analysis of disease association by data-mining of functional annotation of human genes, GENOMICS, Vol: 99, Pages: 1-9, ISSN: 0888-7543
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- Citations: 8
Haberle V, Lenhard B, 2012, Dissecting genomic regulatory elements in vivo., Nat Biotechnol, Vol: 30, Pages: 504-506
de Almeida CR, Stadhouders R, de Bruijn MJW, et al., 2011, The DNA-Binding Protein CTCF Limits Proximal Vκ Recombination and Restricts κ Enhancer Interactions to the Immunoglobulin κ Light Chain Locus, IMMUNITY, Vol: 35, Pages: 501-513, ISSN: 1074-7613
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- Citations: 89
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