GENCODE 2025: reference gene annotation for human and mouse

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D966 - D975

Published: Nov. 20, 2024

GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies methodologies allow us to catalog genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables identify large numbers of missing transcripts substantially improve existing models, our long non-coding RNA catalogs have undergone a dramatic expansion reconfiguration result. Meanwhile, we are incorporating data from state-of-the-art proteomics Ribo-seq experiments fine-tune translated sequences, while further insights into function can be gained multi-genome alignments that grow richer more species' genomes sequenced. Such combined fully integrated workflow. However, increasing complexity resources present usability challenges, resolving these with creation filtered genesets such MANE Select Primary. The next challenge is propagate annotations throughout multiple mouse genomes, enter pangenome era. Our freely available web portal www.gencodegenes.org, via Ensembl UCSC browsers.

Language: Английский

---

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 25, 2024

Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (TF) binding at context-specific cREs remain elusive. We introduce ChromBPNet, a deep learning DNA model base-resolution profiles detects, learns deconvolves assay-specific enzyme biases from regulatory determinants accessibility, enabling robust discovery compact TF motif lexicons, cooperative precision footprints assays sequencing depths. Extensive benchmarks show despite its lightweight design, is competitive much larger contemporary models predicting variant effects on pioneer reporter activity cell ancestry, while providing interpretation disrupted syntax. ChromBPNet also helps prioritize interpret influence complex traits rare diseases, thereby powerful lens to decode variation.

Language: Английский

---

GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 31, 2024

Abstract Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference human mouse genomes, becoming a foundation biomedical genomics communities worldwide. Nevertheless, collections of important yet poorly-understood classes like long non-coding RNAs (lncRNAs) remain incomplete scattered across multiple, uncoordinated catalogs, slowing down progress in field. To address these issues, undertaken most comprehensive lncRNAs annotation effort to date. This is founded on manual full-length targeted long-read sequencing, matched embryonic adult tissues, orthologous regions mouse. Altogether 17,931 novel genes (140,268 transcripts) 22,784 (136,169 have been added catalog representing 2-fold 6-fold increase transcripts, respectively - greatest since sequencing genome. Novel display evolutionary constraints, well-formed promoter regions, link phenotype-associated genetic variants. They greatly enhance functional interpretability genome, as they help explain millions previously-mapped “orphan” omics measurements corresponding transcription start sites, chromatin modifications factor binding sites. Crucially, our design assigned human-mouse orthologs at rate beyond previous studies, tripling number disease-associated with orthologs. The expanded enhanced lncRNA mark critical step towards deciphering genomes.

Language: Английский

---

Rewriting regulatory DNA to dissect and reprogram gene expression

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

---

The role(s) of NF-Y in development and differentiation

Cell Death and Differentiation, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 26, 2024

Language: Английский

---

Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

---