GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing Article Swipe
Gazaldeep Kaur
,
Tamara Perteghella
,
Sílvia Carbonell Sala
,
José M. González
,
Toby Hunt
,
Tomasz Mądry
,
Irwin Jungreis
,
Carme Arnan
,
Julien Lagarde
,
Beatrice Borsari
,
Cristina Sisu
,
Yunzhe Jiang
,
Ruth Bennett
,
Andrew Berry
,
Daniel Cerdán-Vélez
,
Kelly Cochran
,
Covadonga Vara
,
Claire Davidson
,
Sarah Donaldson
,
Cagatay Dursun
,
Silvia González-López
,
Sasti Gopal Das
,
Matthew P. Hardy
,
Zoe Hollis
,
Mike Kay
,
José Carlos Montañés
,
Pengyu Ni
,
Ramil Nurtdinov
,
Emilio Palumbo
,
Carlos Pulido-Quetglas
,
Marie‐Marthe Suner
,
X. Yu
,
Dingyao Zhang
,
Jane Loveland
,
M. Mar Albà
,
Mark Diekhans
,
Andrea Tanzer
,
Jonathan M. Mudge
,
Paul Flicek
,
Fergal J. Martin
,
Mark Gerstein
,
M. Kellis
,
Anshul Kundaje
,
Benedict Paten
,
Michael L. Tress
,
Rory Johnson
,
Barbara Uszczyńska-Ratajczak
,
Adam Frankish
,
Roderic Guigó
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.10.29.620654
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.10.29.620654
Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, becoming a foundation for biomedical and genomics communities worldwide. Nevertheless, collections of important yet poorly-understood gene classes like long non-coding RNAs (lncRNAs) remain incomplete and scattered across multiple, uncoordinated catalogs, slowing down progress in the field. To address these issues, GENCODE has undertaken the most comprehensive lncRNAs annotation effort to date. This is founded on the manual annotation of full-length targeted long-read sequencing, on matched embryonic and adult tissues, of orthologous regions in human and mouse. Altogether 17,931 novel human genes (140,268 novel transcripts) and 22,784 novel mouse genes (136,169 novel transcripts) have been added to the GENCODE catalog representing a 2-fold and 6-fold increase in transcripts, respectively - the greatest increase since the sequencing of the human genome. Novel gene annotations display evolutionary constraints, have well-formed promoter regions, and link to phenotype-associated genetic variants. They greatly enhance the functional interpretability of the human genome, as they help explain millions of previously-mapped “orphan” omics measurements corresponding to transcription start sites, chromatin modifications and transcription factor binding sites. Crucially, our targeted design assigned human-mouse orthologs at a rate beyond previous studies, tripling the number of human disease-associated lncRNAs with mouse orthologs. The expanded and enhanced GENCODE lncRNA annotations mark a critical step towards deciphering the human and mouse genomes.
Related Topics
Concepts
Massive parallel sequencing
Computational biology
Massively parallel
RNA
Computer science
Biology
DNA sequencing
Genetics
DNA
Parallel computing
Gene
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.10.29.620654
- https://www.biorxiv.org/content/biorxiv/early/2024/10/31/2024.10.29.620654.full.pdf
- OA Status
- green
- Cited By
- 17
- References
- 70
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4403988423
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4403988423Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2024.10.29.620654Digital Object Identifier
- Title
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GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencingWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
-
2024-10-31Full publication date if available
- Authors
-
Gazaldeep Kaur, Tamara Perteghella, Sílvia Carbonell Sala, José M. González, Toby Hunt, Tomasz Mądry, Irwin Jungreis, Carme Arnan, Julien Lagarde, Beatrice Borsari, Cristina Sisu, Yunzhe Jiang, Ruth Bennett, Andrew Berry, Daniel Cerdán-Vélez, Kelly Cochran, Covadonga Vara, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Silvia González-López, Sasti Gopal Das, Matthew P. Hardy, Zoe Hollis, Mike Kay, José Carlos Montañés, Pengyu Ni, Ramil Nurtdinov, Emilio Palumbo, Carlos Pulido-Quetglas, Marie‐Marthe Suner, X. Yu, Dingyao Zhang, Jane Loveland, M. Mar Albà, Mark Diekhans, Andrea Tanzer, Jonathan M. Mudge, Paul Flicek, Fergal J. Martin, Mark Gerstein, M. Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Rory Johnson, Barbara Uszczyńska-Ratajczak, Adam Frankish, Roderic GuigóList of authors in order
- Landing page
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https://doi.org/10.1101/2024.10.29.620654Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2024/10/31/2024.10.29.620654.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2024/10/31/2024.10.29.620654.full.pdfDirect OA link when available
- Concepts
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Massive parallel sequencing, Computational biology, Massively parallel, RNA, Computer science, Biology, DNA sequencing, Genetics, DNA, Parallel computing, GeneTop concepts (fields/topics) attached by OpenAlex
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17Total citation count in OpenAlex
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2025: 16, 2024: 1Per-year citation counts (last 5 years)
- References (count)
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70Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.adult | 99 |
| abstract_inverted_index.date. | 82 |
| abstract_inverted_index.genes | 112, 120 |
| abstract_inverted_index.human | 28, 105, 111, 149, 175, 216, 236 |
| abstract_inverted_index.mouse | 30, 119, 220, 238 |
| abstract_inverted_index.novel | 110, 114, 118, 122 |
| abstract_inverted_index.omics | 185 |
| abstract_inverted_index.since | 144 |
| abstract_inverted_index.start | 190 |
| abstract_inverted_index.these | 70 |
| abstract_inverted_index.17,931 | 109 |
| abstract_inverted_index.2-fold | 133 |
| abstract_inverted_index.22,784 | 117 |
| abstract_inverted_index.6-fold | 135 |
| abstract_inverted_index.across | 58 |
| abstract_inverted_index.beyond | 209 |
| abstract_inverted_index.design | 202 |
| abstract_inverted_index.effort | 80 |
| abstract_inverted_index.encode | 13 |
| abstract_inverted_index.factor | 196 |
| abstract_inverted_index.field. | 67 |
| abstract_inverted_index.genome | 11 |
| abstract_inverted_index.lncRNA | 227 |
| abstract_inverted_index.manual | 88 |
| abstract_inverted_index.mouse. | 107 |
| abstract_inverted_index.number | 214 |
| abstract_inverted_index.remain | 54 |
| abstract_inverted_index.sites, | 191 |
| abstract_inverted_index.sites. | 198 |
| abstract_inverted_index.twenty | 17 |
| abstract_inverted_index.years, | 18 |
| abstract_inverted_index.GENCODE | 20, 72, 129, 226 |
| abstract_inverted_index.address | 69 |
| abstract_inverted_index.binding | 197 |
| abstract_inverted_index.catalog | 130 |
| abstract_inverted_index.classes | 48 |
| abstract_inverted_index.display | 154 |
| abstract_inverted_index.enhance | 169 |
| abstract_inverted_index.explain | 180 |
| abstract_inverted_index.founded | 85 |
| abstract_inverted_index.genetic | 165 |
| abstract_inverted_index.genome, | 176 |
| abstract_inverted_index.genome. | 150 |
| abstract_inverted_index.greatly | 168 |
| abstract_inverted_index.issues, | 71 |
| abstract_inverted_index.lncRNAs | 78, 218 |
| abstract_inverted_index.matched | 96 |
| abstract_inverted_index.regions | 103 |
| abstract_inverted_index.slowing | 62 |
| abstract_inverted_index.towards | 233 |
| abstract_inverted_index.(136,169 | 121 |
| abstract_inverted_index.(140,268 | 113 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Accurate | 1 |
| abstract_inverted_index.assigned | 203 |
| abstract_inverted_index.becoming | 32 |
| abstract_inverted_index.complete | 3 |
| abstract_inverted_index.critical | 231 |
| abstract_inverted_index.enhanced | 225 |
| abstract_inverted_index.expanded | 223 |
| abstract_inverted_index.genomes, | 31 |
| abstract_inverted_index.genomes. | 239 |
| abstract_inverted_index.genomics | 38 |
| abstract_inverted_index.greatest | 142 |
| abstract_inverted_index.increase | 136, 143 |
| abstract_inverted_index.millions | 181 |
| abstract_inverted_index.previous | 210 |
| abstract_inverted_index.progress | 64 |
| abstract_inverted_index.promoter | 159 |
| abstract_inverted_index.regions, | 160 |
| abstract_inverted_index.studies, | 211 |
| abstract_inverted_index.targeted | 92, 201 |
| abstract_inverted_index.tissues, | 100 |
| abstract_inverted_index.tripling | 212 |
| abstract_inverted_index.(lncRNAs) | 53 |
| abstract_inverted_index.catalogs, | 61 |
| abstract_inverted_index.chromatin | 192 |
| abstract_inverted_index.developed | 23 |
| abstract_inverted_index.embryonic | 97 |
| abstract_inverted_index.important | 44 |
| abstract_inverted_index.long-read | 93 |
| abstract_inverted_index.multiple, | 59 |
| abstract_inverted_index.orthologs | 205 |
| abstract_inverted_index.reference | 24 |
| abstract_inverted_index.scattered | 57 |
| abstract_inverted_index.sequences | 12 |
| abstract_inverted_index.variants. | 166 |
| abstract_inverted_index.Altogether | 108 |
| abstract_inverted_index.Crucially, | 199 |
| abstract_inverted_index.annotation | 79, 89 |
| abstract_inverted_index.biological | 14 |
| abstract_inverted_index.biomedical | 36 |
| abstract_inverted_index.consortium | 21 |
| abstract_inverted_index.foundation | 34 |
| abstract_inverted_index.functional | 171 |
| abstract_inverted_index.functions. | 15 |
| abstract_inverted_index.incomplete | 55 |
| abstract_inverted_index.non-coding | 51 |
| abstract_inverted_index.orthologs. | 221 |
| abstract_inverted_index.sequencing | 146 |
| abstract_inverted_index.undertaken | 74 |
| abstract_inverted_index.worldwide. | 40 |
| abstract_inverted_index.annotations | 5, 25, 153, 228 |
| abstract_inverted_index.collections | 42 |
| abstract_inverted_index.communities | 39 |
| abstract_inverted_index.deciphering | 234 |
| abstract_inverted_index.full-length | 91 |
| abstract_inverted_index.human-mouse | 204 |
| abstract_inverted_index.orthologous | 102 |
| abstract_inverted_index.sequencing, | 94 |
| abstract_inverted_index.well-formed | 158 |
| abstract_inverted_index.constraints, | 156 |
| abstract_inverted_index.evolutionary | 155 |
| abstract_inverted_index.measurements | 186 |
| abstract_inverted_index.representing | 131 |
| abstract_inverted_index.respectively | 139 |
| abstract_inverted_index.transcripts) | 115, 123 |
| abstract_inverted_index.transcripts, | 138 |
| abstract_inverted_index.“orphan” | 184 |
| abstract_inverted_index.Nevertheless, | 41 |
| abstract_inverted_index.comprehensive | 77 |
| abstract_inverted_index.corresponding | 187 |
| abstract_inverted_index.indispensable | 7 |
| abstract_inverted_index.modifications | 193 |
| abstract_inverted_index.transcription | 189, 195 |
| abstract_inverted_index.uncoordinated | 60 |
| abstract_inverted_index.understanding | 9 |
| abstract_inverted_index.interpretability | 172 |
| abstract_inverted_index.poorly-understood | 46 |
| abstract_inverted_index.previously-mapped | 183 |
| abstract_inverted_index.disease-associated | 217 |
| abstract_inverted_index.phenotype-associated | 164 |
| cited_by_percentile_year.max | 100 |
| cited_by_percentile_year.min | 90 |
| corresponding_author_ids | https://openalex.org/A5067701434 |
| countries_distinct_count | 7 |
| institutions_distinct_count | 49 |
| corresponding_institution_ids | https://openalex.org/I170486558, https://openalex.org/I4210137962 |
| citation_normalized_percentile.value | 0.97490369 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |