Uncovering the Genetic Profiles Underlying the Intrinsic Organization of the Human Cerebellum

Decoding the genetic profiles underlying the cerebellar functional organization is critical for uncovering the essential role of the human cerebellum in various high-order functions and malfunctions in neuropsychiatric disorders. However, no effort has been made to systemically address this. By combining transcriptome data with the intrinsic functional connectivity of the human cerebellum, we not only identified 443 network-specific genes but also discovered that their gene co-expression pattern correlated strongly with intra-cerebellar functional connectivity. Of these genes, 90 were also differentially expressed in the cerebral cortex and linked the cortico-cerebellar cognitive-limbic networks. To further discover the biological functions of these genes, we performed a virtual gene knock-out by observing the change in the coupling between gene co-expression and functional connectivity and divided the genes into two subsets, i.e., a positive gene contribution indicator (GCI+) and a negative gene set (GCI-). GCI+ is mainly involved in cerebellar neurodevelopment, while GCI- is related to neurotransmission and is significantly enriched in various neurological and neuropsychiatric disorders that are closely linked the cerebellar functional abnormalities. Collectively, our results provide new insight into the genetic substrates behind the functional organization of the human cerebellum with relevance to the possible mechanism of cerebellar contributions to related neurological and psychiatric disorders.

Enjoy the Silence: Nearly Half of Human tRNA Genes Are Silent

Transfer RNAs (tRNAs) are key components of the translation machinery. They read codons on messenger RNAs (mRNAs) and deliver the appropriate amino acid to the ribosome for protein synthesis. The human genome encodes more than 500 tRNA genes but their individual contribution to the cellular tRNA pool is unclear. In recent years, novel methods were developed to improve the quantification of tRNA gene expression, most of which rely on next-generation sequencing such as small RNA-Seq applied to tRNAs (tRNA-Seq). In a previous study, we presented a bioinformatics strategy to analyse tRNA-Seq datasets that we named ‘isodecoder-specific tRNA gene contribution profiling’ (Iso-tRNA-CP). Using Iso-tRNA-CP, we showed that tRNA gene expression is cell type- and tissue-specific and that this process can regulate tRNA-derived fragments abundance. An additional observation that stems from that work is that approximately half of human tRNA genes appeared silent or poorly expressed. In this commentary, I discuss this finding in light of the current literature and speculate on potential functions that transcriptionally silent tRNA genes may play. Studying silent tRNA genes may offer a unique opportunity to unravel novel mechanisms of cell regulation associated to tRNA biology.

Asymmetric redundancy of ZERZAUST and ZERZAUST HOMOLOG in different accessions of Arabidopsis thaliana

Divergence among duplicate genes is one of the important sources of evolutionary innovation. But, the contribution of duplicate divergence to variation in Arabidopsis accessions is sparsely known. Recently, we studied the role of a cell wall localized protein, ZERZAUST (ZET), in Landsberg erecta (Ler) accession. Here, we present the study of ZET in Columbia (Col) accession, which not only showed differential expression patterns in comparison to Ler, but also revealed its close homolog, ZERZAUST HOMOLOG (ZETH). Although, genetic analysis implied redundancy, expression analysis revealed divergence, with ZETH showing minimal expression in both Col and Ler. In addition, ZETH shows relatively higher expression levels in Col compared to Ler. Our data also reveal compensatory up-regulation of ZETH in Col, but not in Ler, implying it is perhaps dispensable in Ler. However, a novel CRISPR/Cas9-induced zeth allele confirmed that ZETH has residual activity in Ler. The results provide genetic evidence for accession-specific differences in compensation mechanism and asymmetric gene contribution. Thus, our work reveals a novel example for how weakly expressed homologs contribute to diversity among accessions.

Selección en cruzas interraciales tropicales de maíz de México para adaptación a valles altos

The response of the selection, and its adaptation at high plateaus, of five generations of tropical corn race crosses from Mexico, with a 0- 700 masl altitude range, was evaluated. An assay was planted at Montecillo, Mexico (locale with high plateaus) using four generations of 22 tropical interracial crosses, nine race progenitors and four local populations as controls. Besides of the grain yield per stalk, 15 characters were studied, some as yield components and others as of agronomic interest for its adaptation. The selection for high platea u adaptation with tropical corn inter-racial crosses was efective to increase grain yield per stalk, achiering an average response of 18% per selection cycle, in five cycles. Although with smaller increments, the number of ears per stalk, lenght, diameter and grain percentage of the ear, volume and weight of 100 seeds were modified. Ear and plant height showed undesirable agronomic responses, while days to tasselling, blooming coincidence and plant health improved with the selection. Six crosses in F8 were identified as matching the yield and other characters to the best local control Huamantla (conical race). According to the progenitors used in these crosses, it is deduced that the Tuxpeño race was the largest gene contributor for yield and Vandeño for adaptation genes, while Tepecintle showed a very poor gene contribution to the selection response.