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Chromosome 1

Chromosome 1 is the largest human chromosome, containing approximately 249 million base pairs of DNA and representing nearly 8 percent of the total genetic material in each cell.^[1] It is one of the 23 pairs of chromosomes found in the nucleus of human cells and carries between 2,000 and 2,100 protein-coding genes that provide instructions for producing proteins critical to numerous biological processes, including cell growth, immune response, and neural development.^[1] As the longest chromosome, Chromosome 1 spans from position 1 to 248,956,422 in the reference human genome assembly GRCh38 and is metacentric, with its centromere positioned near the middle, dividing it into a shorter p arm and a longer q arm.^[2] The chromosome is gene-dense relative to its size, harboring a significant proportion of the human proteome, with many genes involved in overlapping coding sequences and regulatory elements that contribute to complex genetic interactions.^[3] Notable genes on Chromosome 1 include those linked to essential functions, such as the tumor suppressor genes in the 1p36 region and the RBM8A gene associated with blood disorders.^[1] Rearrangements, deletions, or duplications in this chromosome are prevalent in various cancers and developmental disorders, underscoring its role in genomic stability.^[3] Chromosome 1 is implicated in several well-characterized genetic conditions due to its high gene content and susceptibility to structural variants. For instance, 1p36 deletion syndrome, resulting from the loss of genetic material at the tip of the short arm, affects approximately 1 in 5,000 newborns and leads to intellectual disability, seizures, and distinctive facial features.^[1] Similarly, 1q21.1 microdeletion syndrome involves the deletion of about 1.35 million base pairs and is associated with developmental delays, heart defects, and increased risk for schizophrenia or autism spectrum disorder.^[1] In oncology, abnormalities like 1p36 deletions occur in roughly 25 percent of neuroblastoma cases, potentially disrupting tumor suppressor functions.^[1] Thrombocytopenia-absent radius (TAR) syndrome, caused by a specific 200-kilobase deletion including the RBM8A gene, results in low platelet counts and limb malformations.^[1] Research on Chromosome 1 has advanced significantly since its complete sequencing in 2006, revealing over 3,000 genes including pseudogenes and highlighting its evolutionary conservation across placental mammals, where it forms a single large unit homologous to parts of multiple chromosomes in other species.^[3]^[4] Ongoing genomic studies, including those from the Human Genome Project and subsequent assemblies, continue to refine annotations, identifying novel transcripts and regulatory regions that influence disease susceptibility and human variation.^[5]

General Characteristics

Size and Composition

Chromosome 1 is the largest autosome in the human genome, encompassing approximately 248,956,422 base pairs and accounting for about 8% of the total genomic DNA.^[2]^[1] This substantial size positions it as a critical component of the 23 pairs of chromosomes that humans inherit, with two copies of chromosome 1—one from each parent—present in every diploid cell.^[1] At its core, chromosome 1 comprises a single linear molecule of double-stranded DNA tightly packaged with histone proteins into nucleosomes, which further condense into chromatin fibers. This organization allows the long DNA strand, which extends roughly 8.5 centimeters when fully uncoiled, to fit within the confines of the cell nucleus during interphase. The chromatin structure not only compacts the genetic material but also regulates access for processes like transcription and replication. Compared to smaller chromosomes, it includes a greater proportion of non-coding DNA regions, which encompass repetitive sequences, introns, and regulatory elements that contribute to genomic stability and function.

Karyotype Position

Chromosome 1 is the largest of the 23 pairs of human chromosomes and is designated as pair 1 in standard G-banding karyotypes, where chromosomes are arranged by decreasing size and centromere position following Giemsa staining.^[1]^[6] This chromosome exhibits a metacentric morphology, characterized by a centromere located near the midpoint, which divides it into a short p arm and a long q arm of approximately equal lengths.^[7]^[8] In visualized karyotypes, chromosome 1 stands out as the longest structure observable under microscopy after staining, underscoring its prominent size relative to other chromosomes.^[6] Chromosome 1 accounts for roughly 8% of the total length of the haploid human genome, spanning approximately 249 million base pairs.^[9] Its completion as the final fully sequenced human chromosome occurred in 2006 through efforts by the Chromosome 1 Consortium, providing a comprehensive reference that advanced the Human Genome Project.^[9]

Structural Features

Arms and Centromere

Chromosome 1 is divided into two arms by its centromere: the short arm, designated as the p arm, which extends from the p telomere to the centromere and spans approximately 125 million base pairs, and the long arm, designated as the q arm, which extends from the centromere to the q telomere and spans approximately 124 million base pairs.^[2] In the GRCh38 reference assembly, the centromere is positioned at the junction of cytogenetic bands 1p11 and 1q11 and is primarily composed of alpha-satellite DNA repeats, which form large arrays essential for kinetochore assembly and proper chromosome attachment to the mitotic and meiotic spindles.^[10] These repeats, organized in higher-order structures, facilitate the recruitment of centromere-specific proteins that ensure accurate chromosome behavior during cell division. Recent complete assemblies, such as T2T-CHM13, have fully resolved these centromeric regions.^[11] At the distal ends of both the p and q arms, telomeres consist of tandem repeats of the TTAGGG sequence, which cap the chromosome ends to prevent enzymatic degradation, end-to-end fusions, and recognition as DNA damage sites.^[12] These protective structures maintain chromosomal stability across multiple cell divisions. Functionally, the centromere coordinates the alignment of chromosomes at the metaphase plate and the subsequent segregation of sister chromatids to daughter cells during mitosis and meiosis.^[13] Disruptions in centromere structure or function, such as altered alpha-satellite integrity or kinetochore assembly errors, can result in chromosome missegregation and aneuploidy, contributing to genomic instability.^[14]

Cytogenetic Bands

Cytogenetic banding is a fundamental technique in human karyotyping that allows for the visual subdivision of chromosomes into distinct regions based on differential staining patterns, facilitating the localization of genetic features and abnormalities on chromosome 1. G-banding, the most commonly used method, involves treating metaphase chromosomes with Giemsa stain after trypsin exposure, producing alternating dark and light bands that reflect underlying chromatin structure and base composition. At the standard 400-band resolution for the haploid karyotype, chromosome 1 exhibits approximately 20-25 visible G-bands, which increases to approximately 40-50 bands at the higher 850-band resolution, enabling finer mapping of structural variants.^[15] Darker G-bands are typically rich in AT base pairs and associated with late-replicating, heterochromatic regions, while lighter R-bands are GC-rich, early-replicating, and more gene-dense.^[16] Prominent examples include the telomeric band 1p36 on the short arm, which is notably gene-dense and euchromatic, often targeted for analysis in structural rearrangements, and the centromere-proximal band 1q21 on the long arm, characterized by heterochromatin and variable copy number, aiding in the detection of deletions or duplications.^[17] These bands serve as reference points within the p and q arms for precise cytogenetic notation according to the International System for Human Cytogenomic Nomenclature (ISCN). Beyond G-banding, complementary techniques enhance resolution: fluorescence in situ hybridization (FISH) uses fluorescent probes to target specific DNA sequences on chromosome 1, allowing sub-band localization, while spectral karyotyping (SKY) employs multicolor labeling to paint each chromosome distinctly, improving identification of complex rearrangements involving chromosome 1.^[18]^[19] In clinical practice, cytogenetic bands on chromosome 1 are essential for pinpointing breakpoints in chromosomal translocations, such as those observed in acute myeloid leukemia, where alterations at specific bands inform prognosis and guide targeted therapies.^[20] This banding framework integrates with molecular data to support diagnostic accuracy in detecting gross chromosomal imbalances without delving into specific disease mechanisms.

Genetic Content

Gene Count and Density

Chromosome 1 harbors approximately 2,000 to 2,100 protein-coding genes based on the latest GENCODE and Ensembl annotations as of 2024-2025 updates. When including non-coding RNA genes such as long non-coding RNAs (lncRNAs), small non-coding RNAs (e.g., miRNAs, snoRNAs), and other regulatory transcripts, the total gene count exceeds 3,000.^[5] These figures derive from comprehensive annotations integrated into the GRCh38 reference genome, with protein-coding genes numbering around 2,059 and non-coding RNAs approximately 1,768 in RefSeq-based counts.^[21] Gene density on chromosome 1 stands at about 8-9 protein-coding genes per megabase (Mb), calculated from its total length of roughly 249 Mb.^[22] This density is lower than that observed on smaller chromosomes, such as chromosome 19 (which has over 15 genes per Mb), but chromosome 1 contributes the largest absolute number of genes across the human genome due to its size.^[5] Overall gene density, incorporating non-coding elements, approaches 13-16 genes per Mb.^[21] The genetic content of chromosome 1 consists of approximately 98% non-coding DNA, which includes vast intronic sequences within genes, intergenic regulatory elements like enhancers and promoters, and pseudogenes. Chromosome 1 exhibits a higher pseudogene count than the genome average, with processed and unprocessed pseudogenes contributing to this elevated number relative to its proportional size.^[23] Estimates of gene counts vary across databases—for instance, NCBI reports around 3,000 total genes, while MedlinePlus emphasizes about 2,000 protein-coding ones—due to differences in annotation criteria and ongoing refinements spurred by the Telomere-to-Telomere (T2T) Consortium's complete gapless assembly of the human genome.^[11]

Notable Genes

Chromosome 1 harbors several genes with critical roles in cellular structure, metabolism, immune signaling, and developmental processes. Among these, the LMNA gene, located at 1q22, encodes the lamin A and lamin C proteins, which form the nuclear lamina—a fibrous network underlying the inner nuclear membrane that provides structural support to the nucleus and facilitates chromatin organization.^[24] The MTHFR gene, situated at 1p36.3, produces methylenetetrahydrofolate reductase, an enzyme essential for folate metabolism that catalyzes the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, thereby supporting homocysteine remethylation to methionine in the one-carbon metabolic pathway.^[25] The RHCE and RHD genes, both positioned at 1p36.11, encode the RhCE and RhD proteins, respectively, which are multipass membrane proteins forming the Rh antigen complex on red blood cells and functioning as ammonium transporters across the erythrocyte membrane.^[26] The IL6R gene at 1q21 encodes the alpha subunit of the interleukin-6 receptor, which binds IL-6 cytokine to initiate classical signaling via the gp130 coreceptor, thereby regulating acute-phase responses and immune cell differentiation.^[27] Similarly, the NOTCH2 gene, located at 1p12, encodes the Notch2 receptor, a transmembrane protein that mediates cell-cell communication through ligand-induced proteolytic cleavage, influencing cell fate determination during embryonic development and tissue homeostasis in vascular, renal, and hepatic systems.^[28] These genes exemplify functional clusters on chromosome 1, including those in immune response pathways (such as IL6R) and developmental signaling (such as NOTCH2), as well as metabolic regulation (such as MTHFR), contributing to the chromosome's high gene density in regions critical for physiological processes.^[29]

Associated Conditions

Genetic Disorders

Chromosome 1 harbors genes implicated in over 350 human diseases, ranging from monogenic conditions to structural abnormalities like deletions and duplications.^[5]^[30] These disorders typically follow autosomal dominant or recessive inheritance patterns, with de novo mutations common in cases involving chromosomal rearrangements.^[31] One prominent structural disorder is 1p36 deletion syndrome, caused by a terminal deletion on the short arm of chromosome 1 that removes approximately 100 genes. This condition leads to intellectual disability, seizures, distinctive facial features, and heart defects, occurring in about 1 in 5,000 newborns.^[32]^[33] Most cases arise de novo, though parental mosaicism can contribute.^[34] Gaucher disease, a lysosomal storage disorder, results from mutations in the GBA gene at 1q22, leading to deficient glucocerebrosidase activity and accumulation of glucocerebroside in cells. It manifests as anemia, bone pain, and organ enlargement in its non-neuronopathic form (type 1), following autosomal recessive inheritance.^[35]^[36] Charcot-Marie-Tooth disease type 1B (CMT1B) is a demyelinating peripheral neuropathy caused by mutations in the MPZ gene at 1q23.3, which encodes myelin protein zero essential for Schwann cell myelin compaction. Symptoms include progressive muscle weakness and sensory loss starting in adolescence, inherited in an autosomal dominant manner.^[37] Certain forms of familial hypercholesterolemia arise from gain-of-function mutations in the PCSK9 gene at 1p32.3, which encodes a protein that degrades low-density lipoprotein receptors, elevating cholesterol levels and increasing cardiovascular risk. This autosomal dominant condition accounts for a subset of cases beyond the primary LDLR locus.^[38]^[39] Hutchinson-Gilford progeria syndrome, a premature aging disorder, stems from mutations in the LMNA gene at 1q22, disrupting nuclear lamina structure via abnormal prelamin A processing. Affected individuals exhibit growth failure, scleroderma-like skin changes, and cardiovascular complications, typically de novo autosomal dominant.^[40]^[41] Early-onset familial Alzheimer's disease can result from mutations in the PSEN2 gene on chromosome 1q42.13, which encodes presenilin-2 involved in amyloid-beta processing; this contrasts with the APP locus on chromosome 21 and follows autosomal dominant inheritance with onset around age 50.^[42]

Cancer Associations

Deletions at the short arm of chromosome 1, particularly at 1p36, are frequently observed in neuroblastomas, where they result in the loss of tumor suppressor genes such as CAMTA1, which inhibits cell growth and activates differentiation programs.^[43] Reduced expression of CAMTA1 correlates with adverse outcomes in neuroblastoma patients, highlighting its role in suppressing tumor progression.^[44] Similarly, 1p36 deletions occur in malignant melanomas, contributing to genomic instability and suggesting the presence of dosage-sensitive tumor suppressors in this region, including CHD5, which regulates chromatin remodeling and cell cycle control.^[45]^[46] Gains and amplifications of the long arm, particularly at 1q, are common in breast and colorectal cancers, driving oncogenesis through overexpression of genes like MDM4 at 1q32, a negative regulator of p53 that promotes cell survival.^[47] These 1q alterations confer growth advantages by suppressing TP53 signaling, with MDM4 amplification mutually exclusive with TP53 mutations in various tumors.^[48] Additionally, 1q gains involve MYC regulators such as BCL9 at 1q21, which enhances Wnt/β-catenin signaling to upregulate MYC transcription and promote tumor progression in breast and colorectal cancers.^[49]^[50] Specific translocations involving chromosome 1, such as t(1;14)(p22;q32), are implicated in lymphomas, particularly mucosa-associated lymphoid tissue (MALT) B-cell lymphomas, where the breakpoint leads to deregulation of BCL10, disrupting NF-κB signaling and promoting lymphomagenesis.^[51] A 2006 genetic mapping of chromosome 1 identified over 350 associations with human diseases, including numerous structural alterations linked to cancer development.^[30] In hematologic malignancies, amplifications at 1q21 are prevalent in multiple myeloma and serve as an independent predictor of poor prognosis, associated with aggressive disease and reduced overall survival regardless of other cytogenetic features.^[52]^[53] These amplifications often involve genes like MCL1, enhancing anti-apoptotic pathways and treatment resistance.^[54] Mechanistically, loss of heterozygosity (LOH) at 1p and 1q arms in various cancers leads to the inactivation of tumor suppressors, disrupting apoptosis and cell cycle regulation; for instance, 1p LOH eliminates genes like CHD5 that maintain chromatin integrity and prevent uncontrolled proliferation, while 1q LOH imbalances oncogene dosage to favor survival signaling.^[46]^[55]

References

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### Summary of Human Chromosome 1
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Human Genome Assembly GRCh38.p14 ; 1, 248,956,422, CM000663.2 ; 2, 242,193,529, CM000664.2 ; 3, 198,295,559, CM000665.2 ; 4, 190,214,555, CM000666.2 ...Missing: protein- coding 2024
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Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent ...
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Human chromosome 1 (Hsa1) represents the largest physical unit in the human genome, comprising some 285 million base pairs—nearly 9% of the entire genome ( ...
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Chromosome 1 is the largest and is over three times bigger than chromosome 22. The 23rd pair of chromosomes are two special chromosomes, X and Y, that determine ...
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We can find many different chromosomes. Chromosome 1 is the largest of the human chromosomes, made up of approximately 249 million base pairs of the ...
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Karyotype of normal human chromosomes. Ideogram showing G-banding (Giemsa staining) patterns of human metaphase chromosomes of a normal male, 46,XY.
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May 18, 2006 · This study reports the finished sequence of human chromosome 1, and provides a detailed annotation of the landscape, gene index and sequence variations of the ...
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Chromosome arm 1p appears to be one of the “hot spots” in the non-neoplastic mucosa that, when deleted, is associated with the initiation of carcinogenesis.
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4853 - Gene ResultNOTCH2 notch receptor 2 [ (human)] - NCBI
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