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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...cord are going through distinct disease mechanisms, owing to differences in target innervation and local environments. We used laser capture microdissection (LCM) and Smart-seq2 RNA sequencing (LCM-seq) (Nichterwitz et al. 2016, 2018) to analyze the transcriptional dynamics across these neuronal...
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Method: Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo
- Luca Tosti,
- James Ashmore,
- Boon Siang Nicholas Tan,
- Benedetta Carbone,
- Tapan K. Mistri,
- Valerie Wilson,
- Simon R. Tomlinson,
- and Keisuke Kaji
Genome Res. April 2018 28: 592-605; Published in Advance March 23, 2018, doi:10.1101/gr.227124.117
...investigation of TF–DNA interactions and GRNs in specific cell types of limited availability in mammals, including in vivo samples.Genome-wide transcription factor (TF) occupancy is commonly assessed by chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq), but the need for both Ch...
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Method: Time course regulatory analysis based on paired expression and chromatin accessibility data
- Zhana Duren,
- Xi Chen,
- Jingxue Xin,
- Yong Wang,
- and Wing Hung Wong
Genome Res. April 2020 30: 622-634; Published in Advance March 18, 2020, doi:10.1101/gr.257063.119
..., respectively. Figure 4D shows the GO enrichment score (defined as the geometric mean of fold change and −log10[P-value]) of known versus novel enhancers’ targets on RA D10. GO terms such as cerebellar granular layer development, synapse assembly, regulation of AMPA receptor activity, and hindbrain...
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Research: Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
- J. Omar Yáñez-Cuna,
- Cosmas D. Arnold,
- Gerald Stampfel,
- Łukasz M. Boryń,
- Daniel Gerlach,
- Martina Rath,
- and Alexander Stark
Genome Res. July 2014 24: 1147-1156; Published in Advance April 8, 2014, doi:10.1101/gr.169243.113
.... Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control.Genome Res 22: 2278–2289. Chang C-C, Lin C-J. 2011. LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol (TIST) 2: 27. Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD...
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Methods: Predicting tissue-specific enhancers in the human genome
- Len A. Pennacchio,
- Gabriela G. Loots,
- Marcelo A. Nobrega,
- and Ivan Ovcharenko
Genome Res. February 2007 17: 201-211; Published in Advance January 8, 2007, doi:10.1101/gr.5972507
...of multicellular complexity; yet the genetic code of vertebrate gene regulation remains poorly understood. In an attempt to elucidate this code, we synergistically combined genome-wide gene-expression profiling, vertebrate genome comparisons, and transcription factor binding-site analysis to define sequence...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...To investigatewhetherCRSs of low SIwere indeed structurally conserved, we performed RNA structure probing (Methods) of homologous human and mouse sequences of 10 CRSs, selected based on their low FDR (∼10%), low SI, and qRT-PCR–validated coexpression in human and mouse brain. In vitro transcription yielded four CRS...
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