GENCODE: The reference human genome annotation for The ENCODE Project

Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M.; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen M. J.; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles A.; Harte, Rachel A.; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael L.; Rodriguez, José Manuel; Ezkurdia, Iakes; Baren, J. Van; Brent, Michael R.; Haussler, David; Kellis, M; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim

doi:10.1101/gr.135350.111

Cited by 4,338 publications

(4,047 citation statements)

References 79 publications

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“…We mapped the RNA-seq data to mm9 reference mouse genome assembly and GENCODE vM1 transcriptome 56 using STAR v.2.5.0a 57 and scripts from the ENCODE RNA-Seq pipeline [https://github.com/ENCODE-DCC/long-rna-seq-pipeline]. To obtain the tracks of local transcription, we aggregated the uniquely mapped reads into RPM-normalized bigWig files using the built-in STAR functionality.…”

Section: On-line Methodsmentioning

confidence: 99%

Two independent modes of chromatin organization revealed by cohesin removal

Schwarzer

Abdennur

Goloborodko

et al. 2017

Nature

1,052

114

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Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-large active and inactive compartments, and partitioning into sub-megabase domains (TADs). Yet, it remains unclear how these layers of organization form, interact with one another and impact genome functions. Here, we show that deletion of the cohesin-loading factor Nipbl, in mouse liver, leads to a dramatic reorganization of chromosomal folding. TADs and associated peaks vanish globally, even in the absence of transcriptional changes. In contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the 3D organization of the genome results from the interplay of two independent mechanisms: 1) cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; 2) cohesin-dependent formation of TADs, possibly by loop extrusion, which contributes to guide distant enhancers to their target genes.

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Section: On-line Methodsmentioning

confidence: 99%

Two independent modes of chromatin organization revealed by cohesin removal

Schwarzer

Abdennur

Goloborodko

et al. 2017

Nature

1,052

114

1,115

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“…After discarding reads shorter than 20 bp, paired‐end reads were mapped to hg38 genome using the splice‐aware algorithm RSEM (v1.2.15; Li & Dewey, 2011) with GENCODE v23 (Harrow et al , 2012) reference annotation and the following parameters: “–bowtie2 –paired‐end”. For T47D TruSeq data, only read1 was used for gene differential analysis and gene function analysis.…”

Section: Methodsmentioning

confidence: 99%

Function of HNRNPC in breast cancer cells by controlling the dsRNA‐induced interferon response

et al. 2018

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Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG‐I was responsible for such tumor‐inhibitory effect. Interestingly, repression of HNRNPC resulted in accumulation of endogenous double‐stranded RNA (dsRNA), the binding ligand of RIG‐I. These up‐regulated dsRNA species were highly enriched by Alu sequences and mostly originated from pre‐mRNA introns that harbor the known HNRNPC binding sites. Such source of dsRNA is different than the recently well‐characterized endogenous retroviruses that encode dsRNA. In summary, essentialness of HNRNPC in the breast cancer cells was attributed to its function in controlling the endogenous dsRNA and the down‐stream interferon response. This is a novel extension from the previous understandings about HNRNPC in binding with introns and regulating RNA splicing.

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“…For each protein coding transcript in the Gencode v. 22 40 , the genomic coordinates of the region between the annotated CDS stop and the next in frame stop were extracted. Any nucleotide position within this region which overlapped with another annotated coding region in the Gencode annotations was discarded.…”

Section: Identification Of Transcripts With Ribosome Footprint Densitmentioning

confidence: 99%