OC 08.4 - Landscape of antisense genes in the human genome and identification of new human hepatic antisense RNAs by long-read sequencing. Relevance in hemostasis.

Saturday, June 22, 2024

13:45 – 14:00 ICT

Room: 211 A-D

Presenting Author(s)

Juan José Rojo-Carrillo

PhD Student
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain

Co-Author(s)

Pedro Garrido-Rodríguez

PhD student
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
ML

María Llamas-López, PhD-Student

Bioinformatician
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
RC

Rosa Cifuentes-Riquelme

Predoctoral student
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
JP

José Padilla

Tech
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
CB

Carlos Bravo-Pérez

PhD MD
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
Belén de la Morena-Barrio, PhD

Post-doc
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
EN

Esther Navarro

Post-doc
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
VV

Vicente Vicente

Senior Researcher
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
ML

María Luisa Lozano

Hematologist
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
Javier Corral

Professor
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain
María Eugenia de la Morena-Barrio, PhD

PhD
Servicio de Hematología, Hospital General Universitario Morales Messeguer, Centro Regional de Hemodonación, Universidad de Murcia, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII
Murcia, Murcia, Spain

Background: 90% of the human genome produces non-coding RNAs, including antisense genes (AS), which are long non-coding genes (transcripts>200 nucleotides) located on the opposite strand of coding genes (sense genes). Thus AS generates RNAs complementary to sense gene RNAs, with a regulatory role. AS have been associated with cardiovascular diseases, cancer, and diabetes.

Aims: To dissect AS in the human genome and identify new AS, focusing on those related to hemostasis.

Methods: AS were identified using Ensembl v106. mRNA from 15 human livers was sequenced using long-read sequencing by nanopore (ONT). De novo assembly and quantification were performed using Flair v1.5.1, and transcripts were classified with Sqanti v4.1.3. Expression levels were measured in transcripts per million (TPM).

Results: The human genome contains 1656 AS overlapping with 1556 sense genes. Genes with AS were larger had more repetitive elements, and exhibited higher transcriptional activity than genes without AS. Only 9 AS were related to hemostasis: 2 coagulation and 7 platelet-related genes (Table-1).
Sequencing of human liver mRNA identified 185 transcripts (55 novel) from 150 AS that had moderate expression (7.7 TPM; IQR=4.3) and 1316 transcripts from 807 sense genes (11.5 TPM; IQR=10.5). Among 111 sense-AS coexpressed pairs, sense transcripts had higher expression. Notably, 696 sense genes lacked coexpression of their AS counterparts, including F10 and F11, and 40 AS were expressed without sense expression. Importantly, 146 transcripts corresponded to 118 potential new AS, none related to coagulation (Figure-1).

Conclusion(s): Systematic analysis of AS in the human genome revealed that 1/10 genes had AS, but nanopore sequencing reveals 118 potential new AS expressed in liver, supporting that the number of AS is underestimated. The low proportion of AS related to coagulation, and the lack of expression in liver, suggests that this mechanism of regulation is not crucial in coagulation.

Funding: PMP21/00052&PI21/00137 (ISCIII&Next Generation UE); 21886/PI/22 (Fundación Séneca).